Materials and methods for diagnosis, prognosis and assessment of therapeutic/prophylactic treatment of prostate cancer

ABSTRACT

A method to detect prostate cancer comprising contacting a sample of prostate cells from the patient with a set of detectably labeled probes under hybridization conditions and determining the presence of chromosomal abnormalities in prostate tumor tissue, PIN (intra-epithelial neoplasia), histologically benign tissue and benign prostatic hyperplasia (BPH); a method to combine immunofluorescence and FISH (IF-FISH) to facilitate the assessment of chromosomal abnormalities; a set of probes; and a kit comprising the set of probes and instructions for diagnosing prostate cancer in a patient.

CROSS REFERENCE TO RELATED APPLICATIONS

This application claims priority to U.S. provisional patent applicationNo. 61/582,212, which was filed on Dec. 30, 2011, and the content ofwhich is hereby incorporated by reference in its entirety.

TECHNICAL FIELD

The present disclosure relates to methods of diagnosis, prognosis andassessment of the therapeutic or prophylactic treatment of cancer, inparticular prostate cancer, the detection of phenotypic and genotypicabnormalities, immunofluorescence, and in situ hybridization, as well asa set of probes and a kit useful in such methods.

BACKGROUND

Prostate cancer is the most common malignancy in men, and, after lungcancer, the second leading cause of death in men. There were anestimated 217,730 new cases in 2010 resulting in 32,050 deaths. Themajority of tumors are confined to the prostate. Others are clinicallylocalized to the peri-prostatic area but extend through the prostaticcapsule and may involve seminal vesicles. The remaining tumors aremetastatic.

The absence of reliable diagnostic markers that enable early andaccurate detection of tumors when they are confined to the prostate, aswell as prognostic markers that enable prediction of diseaseprogression, is a fundamental problem in the management of prostatecancer. Early detection and diagnosis of prostate cancer currentlyrelies on digital rectal examination (DRE), prostate-specific antigen(PSA) measurement, transrectal ultrasonography (TRUS), and transrectalneedle biopsy (TRNB). The leading diagnostic approach employs acombination of DRE and measurement of serum PSA; however, this approachhas major limitations. Detection of an elevation in the level of PSA ismore sensitive than specific (Thompson et al., NEJM 350: 2239-2246(2004)). Consequently, more men are unnecessarily subjected to needlebiopsy due to PSA screening and, unfortunately, the focal nature ofprostate cancer results in needle biopsy sampling errors with falsenegative rates of 15-30% during diagnosis (Campos-Fernandes et al., Eur.Urol. 55: 600-609 (2009)). Out of the approximately 1.2 million patientswho undergo prostate biopsy each year in the U.S., 70-80% receivenegative results but cannot be reassured because a cancer might havebeen missed by sampling error (Norm et al., Prostate 69: 1470-1479(2009)). Therefore, repeat biopsies (second, third or fourth) arenecessary because of continuous elevated PSA levels (Campos-Fernandes etal. (2009), supra).

Besides PSA, other markers and methods have been identified. Forexample, the measurement of the level of amplification of the HER-2/neugene by fluorescent in situ hybridization (FISH) has been disclosed tobe a method of determining the severity of prostate cancer (Int'l Pat.App. Pub. No. WO 1998/045479). The determination of the presence of anamplified 8q24.1-24.2 chromosome band segment has been disclosed to be amethod of diagnosing prostate cancer progression (U.S. Pat. No.5,658,730). The determination of the loss of the 8p21-22 locus, a gainof chromosome 8, and an additional increase of the copy number of c-mycrelative to the centromere copy number has been disclosed to be a methodof prognosticating prostate cancer (U.S. Pat. No. 6,613,510). Thedetermination of the hybridization pattern of a set of chromosomalprobes comprising a probe to the 8p locus, such as 8p21-22, and a probeto the 8q24 locus and correlating the hybridization pattern withprostate cancer diagnosis also has been disclosed (U.S. Pat. App. Pub.No. 2003/0091994). A gain of 8q24 (c-myc) and a loss of heterozygosityof 8p21-22 (LPL) (Bova et al., Cancer Res. 53: 3869-3873 (1993); Kaganet al., Oncogene 11: 2121-2126 (1995); and Emmert-Buck et al., CancerRes. 55: 2959-2962 (1995)) and 10q23 (PTEN) (Yoshimoto et al., Br. J.Cancer 97(5): 678-685 (Sep. 3, 2007; epub Aug. 14, 2007) also has beendescribed. Testing for the loss of heterozygosity at one or more loci onone or more of chromosomes 1-22 has been disclosed as a method ofdetecting a cell with a neoplastic or preneoplastic phenotype (U.S. Pat.App. Pub. No. 2003/0165895). The detection of an increase in the levelof expression of the 20P1F12/TMPRSS2 gene has been disclosed as a methodof identifying prostate cancer (U.S. Pat. No. 7,037,667). The detectionof a break in the sequence of human chromosome 12q24 at the SMRT genelocus using FISH has been disclosed as a method of determining thelikelihood of prostate cancer metastasis (U.S. Pat. No. 7,425,414). Thedetermination of the level of a constituent such as PTEN RNA has beendisclosed as a method for evaluating the presence of prostate cancer(Int'l Pat. App. Pub. No. WO 2008/121132). The detection of an ACSL3-ETSgene fusion has been disclosed as a method of diagnosing prostate cancer(Int'l Pat. App. Pub. No. WO 2009/144460). The detection of the presenceof a gene fusion having a 5′ portion from a transcriptional regulatoryregion of a TMPRSS2 gene and a 3′ portion from an ERG, ETV1 or ETV4 genehas been disclosed as a method of identifying prostate cancer (U.S. Pat.No. 7,718,369), as well as predicting recurrence, progression andmetastatic potential (Int'l Pat. App. Pub. No. WO 2010/056993). Thedetection of the over-expression of PITX2 has been disclosed as a methodfor diagnosing the presence or risk of prostate cancer (Int'l Pat. App.Pub. No. WO 2010/099577). The identification of an increased level of anucleic acid or polypeptide selected from OCT3/4, Nanog, Sox2, c-myc,If4, keratin 8, and uPAR has been disclosed as a method of identifying aprostate carcinoma (In't1 Pat. App. Pub. No. 2011/037643).

In addition to the above, prostate cancer “field effect” has beenstudied by several groups. Using digital image analysis, researchershave identified subtle changes of nuclear morphology in thehistologically benign tissue adjacent to prostate cancer (Qian et al.,Hum. Pathol. 28: 143-148 (1997); and Veltri et al., Clin. Cancer Res.10: 3465-3473 (2004)). Using cDNA microarrays, the difference of geneexpression profile was reported between adjacent normal tissue ofprostate cancer and normal tissue obtained from organ donors (Chandranet al., BMC Cancer 5(1): 45 (2005); Yu et al., J. Clin. Oncol. 22(14):2790-2799 (2004); and Rizzi et al., PLoS ONE 3(10): e3617 (2008)). Usingimmunohistochemistry, protein expression changes of multiple biomarkerswere noticed in near and distant normal and high-grade prostaticintra-epithelial neoplasia (HGPIN) glands. These markers include Mcm-2and Ki67 (Ananthanarayanan et al., BMC Cancer 6: 73 (2006); Santinelliet al., Am. J. Clin. Pathol. 128(4): 657-666 (2007)), α-methylacyl-CoAracemase (AMACR) (Santinelli et al. (2007), supra; and Ananthanarayananet al., Prostate 63(4): 341-346 (2005)), and androgen receptor (AR)(Olapade-Olaopa et al., Clin. Cancer Res. 5(3): 569-576 (1999)), etc.Using laser capture micro-dissection and quantitativemethylation-specific PCR, field effect for gene silencing throughhypermethylation in prostate carcinogenesis was also found by multiplegroups (Mehrothra et al., Prostate 68(2): 152-160 (2008); and Aitchisonet al., Prostate 67(6): 638-644 (2007)). The genes include GSTP1, APC,RASSF1A, HIN-1 and RARb2.

In view of the foregoing, there remains a need for more reliable andinformative diagnostic and prognostic methods in the management ofprostate cancer. The present disclosure seeks to provide a set ofmarkers, as well as methods of use and a kit comprising the set ofmarkers, for the diagnosis, prognosis, and the assessment of thetherapeutic or prophylactic treatment of cancer, in particular prostatecancer. This and other objects and advantages, as well as inventivefeatures, will become apparent from the detailed description providedherein.

SUMMARY

A method of detecting prostate cancer in a patient is provided. Genomicabnormalities in a prostate tumor (malignancy; designated herein “tumorregion of interest (ROI)”) or an adjacent, apparently benign, area of aprostate (designated herein “benign ROI”), such as in one or more tissuesections of a prostate, are identified and assayed in accordance withthe method. In one embodiment, the method comprises contacting a sampleof prostate cells from the patient with a set of detectably labeledprobes comprising a locus-specific probe for MYC, a locus-specific probefor phosphatase and tensin homolog (PTEN), a centromeric probe forchromosome 8, and a centromeric probe for chromosome 7 underhybridization conditions and determining the presence of chromosomalabnormalities, wherein a MYC % gain (% gain is % of cells with MYC>2signals) of greater than 35 (with a range of 2 to 50), a PTEN % loss (%loss is % of cells with <2 signals) of greater than 33 (with a range of29 to 33), a chromosome 8% gain (% gain is % of cells with >2 signals)of greater than 34 (with a range of 32 to 34), and a chromosome 7%abnormal (% abnormal is % of cells with >2 or <2 signals) greater than28 (with a range of 24 to 29) in a sample of prostate cells from a tumorregion of interest (ROI) or a benign ROI of the prostate of the patientindicates that the patient has prostate cancer.

In another embodiment, the method comprises contacting a sample ofprostate cells from the patient with a set of detectably labeled probescomprising a locus-specific probe for MYC, a locus-specific probe forlipoprotein lipase (LPL), a locus-specific probe for PTEN, and acentromeric probe for chromosome 8 under hybridization conditions anddetermining the presence of chromosomal abnormalities. A MYC/LPL % gain(% gain is % of cells with MYC/LPL>1) of greater than 14 (with a rangeof 12 to 22), a chromosome 8% abnormal (% abnormal is % of cells with >2or <2 signals) of greater than 34 (with a range of 26 to 40), a PTEN %loss (% loss is % of cells with <2 signals) of greater than 44 (with arange of 22 to 54), or a MYC/chromosome 8% gain (% gain is % of cellswith MYC/chromosome 8>1) greater than 16 (with a range of 10 to 18) in asample of prostate cells from a tumor region of interest (ROI) of theprostate of the patient indicates that the patient has prostate cancer.Cut-offs of combined “MYC/LPL % Gain or CEP8% Abnorm or PTEN % Loss orMYC/CEP8% Gain” for tumor ROI FISH parameters were chosen in the regionof target performance: the quadrant between 97.1% sensitivity and 96.2%specificity. A MYC/LPL % gain of greater than 18 (with a range of 12 to19), a chromosome 8% abnormal of greater than 32 (with a range of 25 to34), a PTEN % loss of greater than 26 (with a range of 22 to 28), or aMYC/chromosome 8% gain greater than 16 (with a range of 9 to 18) in asample of prostate cells from a benign ROI of the prostate of thepatient indicates that the patient has prostate cancer. Cut-offs ofcombined “MYC/LPL % Gain or CEP8% Abnorm or PTEN % Loss or MYC/CEP8%Gain” for benign ROI FISH parameters were chosen in the region of targetperformance: the quadrant between 80.8% sensitivity and 82.4%specificity.

The sample of prostate cells can be a section of the prostate of thepatient. The section can be formalin-fixed and paraffin-embedded andplaced on a microscope slide. Prior to determining the presence ofchromosomal abnormalities, the method can further comprisemorphologically assessing the section and identifying at least one tumorROI, at least one benign ROI, or at least one tumor ROI and at least onebenign ROI. Alternatively, prior to determining the presence ofchromosomal abnormalities, the method can further comprise assessing thesection by immunofluorescence and identifying at least one tumor ROI.Assessing the section by immunofluorescence can comprise contacting thesection with a detectably labeled anti-α-methylacyl-CoA racemase (AMACR)antibody and detecting over-expression of AMACR, wherein over-expressionof AMACR in a region of the section indicates the presence of a tumorROI. Prior to assessing the section by immunofluorescence, the methodcan further comprise treating the section with heat-induced epitoperetrieval.

A set of probes is also provided. In one embodiment, the set of probescomprises a locus-specific probe for MYC, a locus-specific probe forPTEN, a centromeric probe for chromosome 8, and a centromeric probe forchromosome 7, wherein the set of probes optionally further comprises ananti-AMACR antibody, which can be detectably labeled. In anotherembodiment, the set of probes comprises a locus-specific probe for MYC,a locus-specific probe for LPL, a locus-specific probe for PTEN, and acentromeric probe for chromosome 8. The set of probes optionally furthercomprises an anti-AMACR antibody, which can be detectably labeled.

A kit is also provided. In one embodiment, the kit comprises (a) a setof probes that enables diagnosis of prostate cancer in a patient,wherein the set of probes comprises a locus-specific probe for MYC, alocus-specific probe for PTEN, a centromeric probe for chromosome 8, anda centromeric probe for chromosome 7, and (b) instructions fordiagnosing prostate cancer in a patient, wherein the instructionscomprise determining in a sample of prostate cells obtained from thepatient the presence of chromosomal abnormalities. A MYC % gain (% gainis % of cells with MYC>2 signals) of greater than 35 (with a range of 2to 50), a PTEN % loss (% loss is % of cells with <2 signals) of greaterthan 33 (with a range of 29 to 33), a chromosome 8% gain (% gain is % ofcells with >2 signals) of greater than 34 (with a range of 32 to 34),and a chromosome 7% abnormal (% abnormal is % of cells with >2 or <2signals) greater than 28 (with a range of 24 to 29) in a sample ofprostate cells from a tumor region of interest (ROI) or a benign ROI ofthe prostate of the patient indicates that the patient has prostatecancer. In another embodiment, the kit comprises (a) a set of probesthat enables diagnosis of prostate cancer in a patient, wherein the setof probes comprises a locus-specific probe for MYC, a locus-specificprobe for LPL, a locus-specific probe for PTEN, and a centromeric probefor chromosome 8 and (b) instructions for diagnosing prostate cancer ina patient, wherein the instructions comprise determining in a sample ofprostate cells obtained from the patient the presence of chromosomalabnormalities. A MYC/LPL % gain (% gain is % of cells with MYC/LPL>1) ofgreater than 14 (with a range of 12 to 22), a chromosome 8% abnormal (%abnormal is % of cells with >2 or <2 signals) of greater than 34 (with arange of 26 to 40), a PTEN % loss (% loss is % of cells with <2 signals)of greater than 44 (with a range of 22 to 54), or a MYC/chromosome 8%gain (% gain is % of cells with MYC/chromosome 8>1) greater than 16(with a range of 10 to 18) in a sample of prostate cells from a tumorregion of interest (ROI) of the prostate of the patient indicates thatthe patient has prostate cancer. A MYC/LPL % gain of greater than 18(with a range of 12 to 19), a chromosome 8% abnormal of greater than 32(with a range of 25 to 34), a PTEN % loss of greater than 26 (with arange of 22 to 28), or a MYC/chromosome 8% gain greater than 16 (with arange of 9 to 18) in a sample of prostate cells from a benign ROI of theprostate of the patient indicates that the patient has prostate cancer.The kit can further comprise instructions for morphologically assessinga section of a prostate from a patient and identifying at least onetumor ROI, at least one benign ROI, or at least one tumor ROI and atleast one benign ROI prior to determining the presence of chromosomalabnormalities. Alternatively, the kit can further comprise instructionsfor assessing a section of a prostate from a patient byimmunofluorescence and identifying the presence of a tumor ROI prior todetermining the presence of chromosomal abnormalities, in which case thekit can further comprise an anti-AMACR antibody, which can be detectablylabeled, and the instructions for assessing a section of a prostate froma patient by immunofluorescence can further comprise contacting thesection with detectably labeled anti-AMACR antibody and detectingover-expression of AMACR, wherein over-expression of AMACR in a regionof the section indicates the presence of a tumor ROI. The instructionscan further comprise treating the section with heat-induced epitoperetrieval prior to assessing the section of a prostate from a patient byimmunofluorescence.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1a is a graph of % loss and % gain versus locus of chromosomeenumerator probe (CEP) 8 in benign prostatic hyperplasia (BPH) andcancer specimens (tumor region of interest of tumor ROI).

FIG. 1b is a graph of % loss and % gain versus locus for chromosomeenumerator probe (CEP) 8 in BPH and cancer specimens (benign ROI).

FIG. 2a is a graph of sensitivity vs. 1-specificity (receiver operatingcharacteristic (ROC) curve) for tumor ROI, wherein (▪) is the percentageabnormal for chromosome enumerator probe 8 (CEP 8% Abnorm), (▴) is thepercentage gain of MYC/lipoprotein lipase (LPL) (MYC/LPL % Gain), (●) isthe percentage gain of MYC/CEP 8 (MYC/CEP 8% Gain), and (□) is thepercentage loss of phosphatase and tensin homolog (PTEN) (PTEN % Loss),and (◯) is the combination cut-off of CEP 8, MYC, LPL, and PTEN (4probes cut-off).

FIG. 2b is a graph of sensitivity vs. 1-specificity (ROC curve) forbenign ROI, wherein (▪) is the percentage abnormal for chromosomeenumerator probe 8 (CEP 8% Abnorm), (▴) is the percentage gain ofMYC/lipoprotein lipase (LPL) (MYC/LPL % Gain), (●) is the percentagegain of MYC/CEP 8 (MYC/CEP8% Gain), and (□) is the percentage loss ofphosphatase and tensin homolog (PTEN) (PTEN % Loss), and (◯) is thecombination cut-off of CEP 8, MYC, LPL, and PTEN (4 probes cut-off).

FIG. 3 is a table of diagnostic cut-offs for CEP 8% Abnorm, MYC/LPL %Gain, MYC/CEP8% Gain, and PTEN % Loss.

FIG. 4 is a graph of sensitivity vs. 1-specificity (ROC curve) forindividual FISH parameters (PTEN % Loss, Cep 7% Abnorm, MYC % Gain, andCEP 8% Gain) and the four-probe combination. Data were calculated fromthe FISH evaluation of the 17 benign ROI and 26 BPH specimens. The ROCplot for the four-probe combination is based on the 33 tumor ROI and the26 BPH specimens. The maximum AUC of the ROC curves are shown in thetable.

FIG. 5 is a table of diagnostic cut-offs for PTEN % Loss, Cep 7% Abnorm,MYC % Gain, and CEP 8% Gain.

DETAILED DESCRIPTION

The present disclosure provides a set of markers, as well as a method ofuse and a kit comprising the set of markers, for the diagnosis,prognosis, and the assessment of the therapeutic or prophylactictreatment of cancer, in particular prostate cancer. The following termsare relevant to the present disclosure:

“About” refers to approximately a +/−10% variation from the statedvalue. It is to be understood that such a variation is always includedin any given value provided herein, whether or not specific reference ismade to it.

“Biomarker,” as defined by the National Institutes of Health, is “acharacteristic that is objectively measured and evaluated as anindicator of normal biologic processes, pathogenic processes, orpharmacologic responses to a therapeutic intervention.”

“Chromosome enumeration probe (CEP)” or “centromeric probe” is any probethat enables the number of specific chromosomes in a cell to beenumerated. A chromosome enumeration probe typically recognizes andbinds to a region near to (referred to as “peri-centromeric”) or at thecentromere of a specific chromosome, typically a repetitive DNA sequence(e.g., alpha satellite DNA). The centromere of a chromosome is typicallyconsidered to represent that chromosome, since the centromere isrequired for faithful segregation during cell division. Deletion oramplification of a particular chromosomal region can be differentiatedfrom loss or gain of the whole chromosome (aneusomy), within which itnormally resides, by comparing the number of signals corresponding tothe particular locus (copy number) to the number of signalscorresponding to the centromere. One method for making this comparisonis to divide the number of signals representing the locus by the numberof signals representing the centromere. Ratios of less than one indicaterelative loss or deletion of the locus, and ratios greater than oneindicate relative gain or amplification of the locus. Similarly,comparison can be made between two different loci on the samechromosome, for example on two different arms of the chromosome, toindicate imbalanced gains or losses within the chromosome. In lieu of acentromeric probe for a chromosome, one of skill in the art willrecognize that a chromosomal arm probe may alternately be used toapproximate whole chromosomal loss or gain. However, such probes are notas accurate at enumerating chromosomes, since the loss of signals forsuch probes may not always indicate a loss of the entire chromosome.Examples of chromosome enumeration probes include CEP® probescommercially available from Abbott Molecular, Inc., Des Plaines, Ill.(formerly Vysis, Inc., Downers Grove, Ill.).

“Copy number” is a measurement of DNA, whether of a single locus, one ormore loci, or an entire genome. A “copy number” of two is “wild-type” ina human (because of diploidy, except for sex chromosomes). A “copynumber” of other than two in a human (except for sex chromosomes)deviates from wild-type. Such deviations include amplifications, i.e.,increases in copy numbers, and deletions, i.e., decreases in copynumbers and even the absence of copy numbers.

“Labeled,” “labeled with a detectable label,” and “detectably labeled”are used interchangeably herein to indicate that an entity (e.g., aprobe) can be detected. “Label” and “detectable label” mean a moietyattached to an entity to render the entity detectable, such as a moietyattached to a probe to render the probe detectable upon binding to atarget sequence. The moiety, itself, may not be detectable but maybecome detectable upon reaction with yet another moiety. Use of the term“detectably labeled” is intended to encompass such labeling. Thedetectable label can be selected such that the label generates a signal,which can be measured and the intensity of which is proportional to theamount of bound entity. A wide variety of systems for labeling and/ordetecting molecules, such as nucleic acids, e.g., probes, arewell-known. Labeled nucleic acids can be prepared by incorporating orconjugating a label that is directly or indirectly detectable byspectroscopic, photochemical, biochemical, immunochemical, electrical,optical, chemical or other means. Suitable detectable labels includeradioisotopes, fluorophores, chromophores, chemiluminescent agents,microparticles, enzymes, magnetic particles, electron dense particles,mass labels, spin labels, haptens, and the like. Fluorophores andchemiluminescent agents are preferred herein.

“Locus-specific probe” and “locus-specific identifier (LSI)” may be usedinterchangeably herein to refer to a probe that selectively binds to aspecific locus in a region on a chromosome, e.g., a locus that has beendetermined to undergo gain/loss in metastasis. A probe can target codingor non-coding regions, or both, including exons, introns, and/orregulatory sequences, such as promoter sequences and the like.

“Nucleic acid sample” refers to a sample comprising nucleic acid in aform suitable for hybridization with a probe, such as a samplecomprising nuclei or nucleic acids isolated or purified from suchnuclei. The nucleic acid sample may comprise total or partial (e.g.,particular chromosome(s)) genomic DNA, total or partial mRNA (e.g.,particular chromosome(s) or gene(s)), or selected sequence(s). Condensedchromosomes (such as are present in interphase or metaphase) aresuitable for use as targets in in situ hybridization, such as FISH.

“Predetermined cutoff” and “predetermined level” refer generally to acutoff value that is used to assess diagnostic/prognostic/therapeuticefficacy results by comparing the assay results against thepredetermined cutoff/level, where the predetermined cutoff/level alreadyhas been linked or associated with various clinical parameters (e.g.,severity of disease, progression/nonprogression/improvement, etc.).

“Probe,” in the context of the present disclosure, is an oligonucleotideor polynucleotide that can selectively hybridize to at least a portionof a target sequence under conditions that allow for or promoteselective hybridization. In general, a probe can be complementary to thecoding or sense (+) strand of DNA or complementary to the non-coding oranti-sense (−) strand of DNA (sometimes referred to as“reverse-complementary”). Probes can vary significantly in length. Alength of about 10 to about 100 nucleotides, such as about 15 to about75 nucleotides, e.g., about 15 to about 50 nucleotides, can be preferredin some applications, whereas a length of about 50-1×10⁵ nucleotides canbe preferred for chromosomal probes and a length of about 25,000 toabout 800,000 nucleotides can be preferred for locus-specific probes.

“Prostate cancer” includes all types of prostate cancer, such asadenocarcinoma, small cell carcinoma, squamous cell carcinoma, sarcoma,and transitional cell carcinoma. The majority of prostate cancer (around95%) is adenocarcinoma. Prostate cancer is distinguished from prostaticintra-epithelial neoplasia (PIN, which is further distinguished aslow-grade or high-grade), which is a precursor to prostate cancer. Smallcell carcinoma and squamous cell carcinoma tend to be very aggressive innature and do not lead to an increase in prostate-specific antigen(PSA). Transitional cell carcinoma rarely develops in the prostate butderives from primary tumors in the bladder and/or urethra.

“Selectively hybridize to” (as well as “selective hybridization,”“specifically hybridize to,” and “specific hybridization”), in thecontext of the present disclosure, refers to the binding, duplexing, orhybridizing of a nucleic acid molecule preferentially to a particularnucleotide sequence under stringent conditions. The term “stringentconditions” refers to conditions under which a probe will hybridizepreferentially to its target sequence, and to a lesser extent to, or notat all to, other non-target sequences. A “stringent hybridization” and“stringent hybridization wash conditions” in the context of nucleic acidhybridization (e.g., as in array, Southern hybridization, Northernhybridization, or FISH) are sequence-dependent, and differ underdifferent conditions.

An extensive guide to the hybridization of nucleic acids is found in,e.g., Tijssen, Laboratory Techniques in Biochemistry and MolecularBiology—Hybridization with Nucleic Acid Probes, Part I, Ch. 2, “Overviewof principles of hybridization and the strategy of nucleic acid probeassays,” Elsevier, N.Y. (1993) (“Tijssen”). Generally, highly stringenthybridization and wash conditions are selected to be about 5° C. lowerthan the thermal melting point (T_(m)) for the specific sequence at adefined ionic strength and pH. The T_(m) is the temperature (underdefined ionic strength and pH) at which 50% of the target sequencehybridizes to a perfectly matched probe. Very stringent conditions areselected to be equal to the T_(m) for a particular probe. An example ofstringent hybridization conditions for hybridization of complementarynucleic acids, which have more than 100 complementary residues, on anarray or on a filter in a Southern or Northern blot is 42° C. usingstandard hybridization solutions (see, e.g., Sambrook and Russell,Molecular Cloning: A Laboratory Manual, 3rd ed., Vol. 1-3, Cold SpringHarbor Laboratory, Cold Spring Harbor Press, NY (2001)).

“Target sequence,” “target region,” and “nucleic acid target” refer to anucleotide sequence that resides at a specific chromosomal locationwhose loss and/or gain, for example, is being determined.

The terminology used herein is for the purpose of describing particularembodiments only and is not otherwise intended to be limiting.

Methods of Detecting, Diagnosing, Prognosticating, and Monitoring theEfficacy of Therapeutic/Prophylactic Treatment of Prostate Cancer

A method of detecting prostate cancer in a patient is provided. In oneembodiment, the method comprises contacting a sample of prostate cellsfrom the patient with a set of detectably labeled probes comprising alocus-specific probe for MYC, a locus-specific probe for phosphatase andtensin homolog (PTEN), a centromeric probe for chromosome 8, and acentromeric probe for chromosome 7 under hybridization conditions anddetermining the presence of chromosomal abnormalities, wherein a MYC %gain (% gain is % of cells with MYC>2 signals) of greater than 35 (witha range of 2 to 50), a PTEN % loss (% loss is % of cells with <2signals) of greater than 33 (with a range of 29 to 33), a chromosome 8%gain (% gain is % of cells with >2 signals) of greater than 34 (with arange of 32 to 34), and a chromosome 7% abnormal (% abnormal is % ofcells with >2 or <2 signals) greater than 28 (with a range of 24 to 29)in a sample of prostate cells from a tumor region of interest (ROI) or abenign ROI of the prostate of the patient indicates that the patient hasprostate cancer. In another embodiment, the method comprises contactinga sample of prostate cells, such as a tissue section or cells obtainedtherefrom, from the patient with a set of detectably labeled probescomprising a locus-specific probe for MYC, a locus-specific probe forlipoprotein lipase (LPL locus), a locus-specific probe for PTEN locus,and a centromeric probe for chromosome 8 under hybridization conditionsand determining the presence of chromosomal abnormalities. A MYC/LPL %gain (% gain is % of cells with MYC/LPL>1) of greater than 14 (with arange of 12 to 22), a chromosome 8% abnormal (% abnormal is % of cellswith >2 or <2 signals) of greater than 34 (with a range of 26 to 40), aPTEN % loss (% loss is % of cells with <2 signals) of greater than 44(with a range of 22 to 54), or a MYC/chromosome 8% gain (% gain is % ofcells with MYC/chromosome 8>1) greater than 16 (with a range of 10 to18) in a sample of prostate cells from a tumor ROI of the prostate ofthe patient indicates that the patient has prostate cancer. A MYC/LPL %gain of greater than 18 (with a range of 12 to 19), a chromosome 8%abnormal of greater than 32 (with a range of 25 to 34), a PTEN % loss ofgreater than 26 (with a range of 22 to 28), or a MYC/chromosome 8% gaingreater than 16 (with a range of 9 to 18) in a sample of prostate cellsfrom a benign ROI of the prostate of the patient indicates that thepatient has prostate cancer. Cutoffs of combined “MYC/LPL % Gain orCEP8% Abnorm or PTEN % Loss or MYC/CEP8% Gain” for tumor ROI FISHparameters were chosen in the region of target performance: the quadrantbetween 97.1% sensitivity and 96.2% specificity. Cutoffs of combined“MYC/LPL % Gain or CEP8% Abnorm or PTEN % Loss or MYC/CEP8% Gain” forbenign ROI FISH parameters were chosen in the region of targetperformance: the quadrant between 80.8% sensitivity and 82.4%specificity.

The set of probes can further comprise one or more of a locus-specificprobe for p16 (9p21), TMPRSS2-ERG or ETV1 fusions (21q22; 7p21 locus), acentromeric probe for chromosome 3, a centromeric probe for chromosome7, a centromeric probe for chromosome 10, and a centromeric probe forchromosome 17. The set of detectably labeled probes can further compriseone or more of a locus-specific probe for cyclin-dependent kinaseinhibitor p27Kip1 (4q43), a locus-specific probe for cyclin-dependentkinase 2 (CDK2; 12q13), a locus-specific probe for cyclin E (CCNE1;19q12 and CCNE2; 8q22), a locus-specific probe for retinoblastoma 1(Rb1; 13q14), a locus-specific probe for NK3 homeobox 1 (NKX3.1;8p21.2), a locus-specific probe for epidermal growth factor receptor(EGFR; 7p11), a locus-specific probe for phosphoinositide-3-kinase(PI3K; 3q26), a locus-specific probe for AKT1 kinase (Akt1; 14q32), alocus-specific probe for FKHR (FOXO1; 13q14.11), a locus-specific probefor p53 binding protein homolog (MDM2; 12q14.3-12q15), a locus-specificprobe for p53 (17p13.1), a locus-specific probe for v-Ki-ras2 Kirstenrat sarcoma viral oncogene homolog (KRAS; 12p12.1), a locus-specificprobe for v-raf murine sarcoma viral oncogene homolog B1 (BRAF; 7q34), alocus-specific probe for cyclin D1 (CCND1; 11q13), a locus-specificprobe for B-cell CLL/lymphoma 2 (BCL2; 18q21.3/18q21.33), and alocus-specific probe for androgen receptor (AR; Xq12).

A method of histological sample pretreatment and hybridization forprostate cancer is provided. FFPE (Formalin Fixed Paraffin Embedded)histological specimens slides (sections) were baked at 56° C. for 2-24hrs, then were pretreated two to three times in Hemo-De (ScientificSafety Solvents) or Xyline for 5 to 10 minutes each at room temperaturefollowed by two 1-minute rinses in 100% ethanol at room temperature,incubation in 45% formic acid/0.3% hydrogen peroxide for 15 minutes atroom temperature and then rinsed in deionized water for 3-10 minutes.Slides were then incubated in pre-treatment solution (1×SSC, PH6.3) at80+/−5° C. for 35-50 minutes, rinsed for 3 minutes in deionized water,incubated 22+/−5 minutes in 0.15% pepsin in 0.1N HCl solution at 37° C.,and rinsed again for 3 minutes in deionized water. Slides weredehydrated for 1 minute each in 70%, 85%, and 100% ethanol and then airdried. Ten microliters of each respective probe hybridization mix (LSI®buffer, blocking DNA, labeled probes) were added to the specimens, acoverslip applied, and sealed with rubber cement. Slides werecodenatured for 5 minutes at 73+/−2° C. and hybridized for 10-24 hoursat 37° C. on a ThermoBrite (Vysis/Abbott Molecular, Inc.). Followinghybridization, coverslips were removed. The sample could be placed inthe wash solution consisting of 0.3×-2×SSC & 0.3%-0.5% NP-40, and thetemperature of the sample can be raised to about 73° C. for about 2-5minutes. Then the support carrying the sample can be eithercounterstained with a nuclear DNA-binding stain, such as4′,6-diamidino-2-phenylindole (DAPI) either in solution, or upon dryingthe sample in the dark. In the latter case, the sample is counterstainedwith about 10 μL DAPI, and a new overslip is placed over the sample. Thesample can then be viewed or stored, e.g., at about −20° C.

A method of prostate FFPE slide IF-FISH procedure is provided. For theassay of simultaneous FISH and Immunofluorescence (IF) on the same FFPEprostate solid tumor tissue slides, a specimen pre-treatment/antigenretrieval protocol was developed and optimized for best results on theFFPE tissue for IF-FISH.

The first step of this procedure is antigen retrieval. Bake prostatecancer FFPE slides at 56° C. for two hours to overnight. De-paraffinizeby two immersions in Hemo-De for 10 minutes each. Incubate twice in 100%ethanol for two minutes each. Hydrate by placing in 85%, 70%, 50%, and30% ethanol for two minutes each. Immerse in molecular grade Milli-Qwater for five minutes. Pre-heat water bath with Coplin jar containingsodium citrate buffer (Sodium Citrate Buffer: 10 mM sodium citrate,0.05% Tween 20, pH 6.0) until temperature reaches 96+/−4° C. Incubatefor 20-60 minutes. Cool at room temperature for 20-40 minutes on bench.Wash slides for five minutes in Milli-Q water. Rinse once for fiveminutes in phosphate-buffered saline (PBS).

The second step is the immunoflorescence (IF) with AMACR antibody andTyramide Signal Amplification Assay (34). Use the Tyramide SolutionAssay (TSA) kit and follow the Alexa Fluor 488 TSA (tyramide signalamplification) kit number 2 (Invitrogen, Molecular Probes) following themanufacturer's directions. Endogenous peroxidase activity is blocked byincubation in 3% H₂O₂ for 30 minutes at room temperature. Add blockingreagent (100 μL/slide) with incubation in a humidified box for 30minutes at room temperature. Add 100 uL of diluted AMACR rabbit antibody(diluted in 1% blocking reagent at 1:100) with incubation for one hourat room temperature. Wash slides three times in PBS/0.1% Tween 20 forfive minutes each. Dilute the stock HRP conjugate solution 1:100 in 1%blocking solution. A 100 μL volume of this working solution issufficient to cover a standard 22×22 mm coverslip. Incubate for 30minutes at room temperature. Wash three times in PBS/0.1% Tween 20 forfive minutes each. Wash once in PBS. Add 100 μL of tyramide solution perslide followed by incubation for 10 minutes at room temperature in thedark. Wash slides in PBS for five minutes. Wash slides for five minutesin Milli-Q water. Proceed to FISH.

The third step is FISH assay. Dehydrate slides in alcohol (70%, 85% and100%, 1 min each), and allow to completely air dry. Add 10 μL of probesolution to each slide, and seal the coverslip over the slide withrubber cement. Co-denature probe and target DNA at 73° C. for fiveminutes followed by hybridization overnight at 37° C. The sample can beplaced in the wash solution consisting of 0.3×-2×SSC and 0.3%-0.5%NP-40, and the temperature of the sample can be raised to about 73° C.for about 2-5 minutes. Then the support carrying the sample can beeither counterstained with a nuclear DNA-binding stain, such as4′,6-diamidino-2-phenylindole (DAPI) either in solution, or upon dryingthe sample in the dark. In the latter case, the sample is counterstainedwith about 10 μL DAPI, and a new coverslip is placed over the sample.The sample can then be viewed or stored, e.g., at about −20° C.

With regard to all of the above methods, the nature/size of the probewill depend, at least in part, on the method used to determine aparticular parameter, e.g., copy number, copy number ratio, orpercentage gain of a gene of interest. When an abovediagnostic/prognostic method is carried out by in situ hybridization,such as FISH, for example, the probe can be relatively large. When anabove diagnostic/prognostic method is carried by another method, theprobe can be smaller, even substantially smaller, than the probe usedfor in situ hybridization, such as FISH, in which case the probepreferably hybridizes to a sequence within the gene of interest.

In view of the above, a probe for detecting a parameter involving MYC,for example, such as the copy number of MYC, a copy number ratioinvolving MYC, or the percentage gain of MYC, by in situ hybridization,such as FISH, preferably hybridizes to the 8q24 region of chromosome 8,which comprises the MYC gene. The probe also can hybridize to anadjacent region located on the centromeric side of 8q24, an adjacentregion located on the telomeric side of 8q24, or both. A preferred probecovers approximately 820 kb, such as 821 kb, of 8q24 and is centered onthe MYC gene. A probe for detecting a parameter involving MYC by anothermethod can be smaller, even substantially smaller, than the probe usedfor in situ hybridization, such as FISH, in which case the probepreferably hybridizes to a sequence within the MYC gene (sequenceinformation is available online from sources such as GenBank andGeneCards® “MYC” is used herein to refer to any and all probes that canbe used to determine a parameter involving MYC, whether copy number,copy number ratio, percentage gain, and the like, irrespective of theparticular method used to determine the parameter.

Like “MYC,” “LPL” is used herein to refer to any and all probes that canbe used to determine a parameter involving LPL, whether copy number,copy number ratio, percentage gain, and the like, irrespective of theparticular method used to determine the parameter. “LPL” includes aprobe that preferably hybridizes to the p22 region of chromosome 8,which comprises the LPL gene. The LPL probe also can hybridize to anadjacent region located on the centromeric side of 8p22, an adjacentregion located on the telomeric side of 8p22, or both. A preferred LPLprobe covers approximately 170 kb of 8p22 and is centered on the LPLgene. “PTEN” is used herein to refer to any and all probes that can beused to determine a parameter involving PTEN, whether copy number, copynumber ratio, percentage gain, and the like, irrespective of theparticular method used to determine the parameter. “PTEN” includes aprobe that preferably hybridizes to the q23 region of chromosome 10,which comprises the PTEN gene. The PTEN probe also can hybridize to anadjacent region located on the centromeric side of 10q23, an adjacentregion located on the telomeric side of 10q23, or both. A preferred PTENprobe covers approximately 365-370 kb, such as 368 kb of 10q23 and iscentered on the PTEN gene. Adjacent regions of the PTENE gen include STSmarkers D10S215 on the centromeric side and RH93626 on the telomericside. The usage of probe designations as explained above applies tomethods, probes and kits discussed herein. The same usage applies toother probe designations set forth herein. As indicated above for theMYC gene, sequence information for the genes recited herein is availableonline from sources such as GenBank and GeneCards®.

The sample of prostate cells is a section of the prostate of thepatient. The sample, such as a tissue section, can be obtained bysurgical resection, needle biopsy, trans-urethral resection of prostate(TURP), or a similar technique. The section can be formalin-fixed andparaffin-embedded and placed on a microscope slide. Alternatively, asection preserved by other means, such as freezing, can be used.

Prior to determining the presence of chromosomal abnormalities, themethod can further comprise morphologically assessing the section andidentifying at least one tumor ROI, at least one benign ROI, or at leastone tumor ROI and at least one benign ROI. Alternatively, prior todetermining the presence of chromosomal abnormalities, the method canfurther comprise assessing the section by immunofluorescence andidentifying at least one tumor ROI. Assessing the section byimmunofluorescence can comprise contacting the section with a detectablylabeled anti-α-methylacyl-CoA racemase (AMACR) antibody and detectingover-expression of AMACR, wherein over-expression of AMACR in a regionof the section indicates the presence of a tumor ROI. Prior to assessingthe section by immunofluorescence, the method can further comprisetreating the section with heat-induced epitope retrieval.

The above method can be carried out using any suitable detection methodknown in the art. Preferably, the above method is carried out using insitu hybridization, such as fluorescent in situ hybridization (FISH).Preferably, each probe is detectably labeled with a distinct label, suchas a distinct fluorophore. Alternatively, radiolabeled nucleotidedetection (in situ hybridization (ISH)), chromomeric hybridizationdetection, and the like, as described herein, can be used.

When the above methods are carried out by in situ hybridization, inwhich each probe is detectably labeled with a distinct label, such as byFISH, in which each probe is labeled with a distinct fluorophore, themethods can be carried out on a sample of prostate cells, which arefresh, such as fresh cells from a biopsy of the prostate (fresh cellscan be cultured for 1-3 days and a blocker, such as Colcemid, can beadded to the culture to block the cells in metaphase, during whichchromosomes are highly condensed and can be visualized), frozen, orfixed (e.g., fixed in formalin and embedded in paraffin), treated (e.g.,with RNase and pepsin) to increase accessibility of target nucleic acid(e.g., DNA) and reduce non-specific binding, and then subjected tohybridization with one or more probes, washing to remove any unboundprobes, and detection of hybridized probes. For example, a cellsuspension can be applied as a single layer onto a slide, and the celldensity can be measured by a light or phase contrast microscope. Cellsalso can be obtained from other sources, such as bodily fluids, e.g.,urine or semen, preserved in fixatives, such as methanol-acetic acid(Carnoy's reagent), and applied to a slide or similar support formicroscopic examination and analysis.

Alternatively, a section (approximately 4-6 μm in thickness) of tissue,such as a section of a formalin-fixed, paraffin-embedded (FFPE) sampleof prostate tissue, can be mounted onto a slide, such as a SuperFrostPlus positively charged slide (available from ThermoShandon, Pittsburgh,Pa.), baked at 56° C. 2 hours to 24 hours (overnight). For FISH assay,sections are then de-paraffinized by pretreating two to three times inHemo-De (Scientific Safety Solvents, Keller, Tex.) or Xyline for 5 to 10minutes each at room temperature, followed by rinsing twice in 100%ethanol at room temperature for one minute each rinse, incubating in 45%formic acid/0.3% hydrogen peroxide for 15 minutes at room temperature,and then rinsing in deionized water for 3-10 minutes. Slides are thenincubated in pre-treatment solution (1×SSC, PH6.3) at 80+/−5° C. for35-50 minutes, rinsed for 3 minutes in deionized water, incubated 22+/−5minutes in 0.15% pepsin in 0.1N HCl solution at 37° C., and rinsed againfor 3 minutes in deionized water. Slides are then dehydrated for 1minute each in 70%, 85%, and 100% ethanol and then air dried.

Ten microliters of each respective probe hybridization mix (LSI® buffer,blocking DNA, and labeled probes) are added to the specimens, andcoverslips are applied and sealed with rubber cement. Slides arecodenatured for five minutes at 73+/−2° C. and hybridized for 10-24hours at 37° C. on a ThermoBrite (Vysis/Abbott Molecular, Inc.).Following hybridization, coverslips are removed. The sample is placed inthe wash solution consisting of 0.3×-2×SSC and 0.3%-0.5% NP-40, and thetemperature of the sample is raised to about 73° C. for about 2-5minutes. Then the support carrying the sample can be eithercounterstained with a nuclear DNA-binding stain, such as4′,6-diamidino-2-phenylindole (DAPI) in solution or upon drying thesample in the dark. In the latter case, the sample is counterstainedwith about 10 μL DAPI, and a new overslip is placed over the sample. Thesample can then be viewed or stored, e.g., at about −20° C.

In this regard, heat-induced epitope retrieval (HIER) can be performed,allowing for simultaneous immunofluorescence and FISH. For the assay ofsimultaneous FISH and Immunofluorescence (IF) on the same FFPE prostatesolid tumor tissue slides, a specimen pre-treatment/antigen retrievalprotocol was developed and optimized for best results on the FFPE tissuefor IF-FISH.

The first step of this procedure is antigen retrieval. Prostate cancerFFPE slides are baked at 56° C. for 2 hours to overnight. Slides arethen de-paraffinized by two immersions in Hemo-De for 10 minutes each.Slides are then incubated in 100% ethanol twice for 2 minutes each time.Slides are hydrated by placing in 85%, 70%, 50%, 30% ethanol for 2minutes each, and a final 5-minute immersion in molecular grade Milli-Qwater. A water bath is pre-heated with a Coplin jar containing sodiumcitrate buffer (10 mM sodium citrate, 0.05% Tween 20, pH 6.0) until thetemperature reaches 96+/−4° C. Slides are then incubated for 20-60minutes, and cooled at room temperature for 20-40 minutes on the bench.Slides are washed for five minutes in Milli-Q water and rinsed once forfive minutes in PBS.

The second step is the immunoflorescence (IF) with AMACR antibody andTyramide Signal Amplification Assay. The Tyramide Solution Assay (TSA)kit and the Alexa Fluor 488 TSA (tyramide signal amplification) kitnumber 2 (Invitrogen, Molecular Probes) are used following themanufacturer's directions. Endogenous peroxidase activity is blocked byincubation in 3% H₂O₂ for 30 minutes at room temperature. Blockingreagent (100 μL/slide) is added, and the slides are incubated in ahumidified box for 30 minutes at room temperature. One hundredmicroliters of diluted AMACR rabbit antibody (diluted in 1% blockingreagent at 1:100) are added, and the slides are incubated for 1 hour atroom temperature. Slides are washed three times for five minutes each inPBS/0.1% Tween 20. Stock HRP conjugate solution is diluted 1:100 in 1%blocking solution. A 100 μL volume of this working solution issufficient to cover a standard 22×22 mm coverslip. Slides are incubatedat room temperature for 30 minutes, and then washed three times inPBS/0.1% Tween 20 for five minutes each wash, followed by one wash inPBS. Tyramide solution (100 μL) is added to each slide, and the slidesare incubated at room temperature for ten minutes in the dark. Theslides are washed for five minutes in PBS and then washed for fiveminutes in Milli-Q water.

The third step is FISH assay. Slides are dehydrated in alcohol (70%, 85%and 100%, 1 min each), and allowed to air dry completely. Probe solution(10 μL) is added to each slide, and a coverslip is sealed over the slidewith rubber cement. Probe and target DNA are denatured at 73° C. forfive minutes followed by hybridization overnight at 37° C. The samplethen can be placed in a wash solution consisting of 0.3×-2×SSC and0.3%-0.5% NP-40, and the temperature of the sample can be raised toabout 73° C. for about 2-5 minutes. Then the support carrying the samplecan be either counterstained with a nuclear DNA-binding stain, such as4′,6-diamidino-2-phenylindole (DAPI) in solution or upon drying thesample in the dark. In the latter case, the sample is counterstainedwith about 10 μL DAPI, and a new coverslip is placed over the sample.The sample can then be viewed or stored, e.g., at about −20° C.

Prior to detection, cell samples may be optionally pre-selected based onapparent cytologic abnormalities. Pre-selection identifies suspiciouscells, thereby allowing the screening to be focused on those cells.Pre-selection allows for faster screening and increases the likelihoodthat a positive result will not be missed. Preferably, regions ofinterest on prostate specimen slides are identified by detectingover-expression of α-methylacyl-CoA racemase (AMACR) using IF and ananti-AMACR antibody. Alternatively, cells from a biological sample canbe placed on a microscope slide and visually scanned for cytologicabnormalities commonly associated with dysplastic and neoplastic cells.Such abnormalities include abnormalities in nuclear size, nuclear shape,and nuclear staining, as assessed by counterstaining nuclei with nucleicacid stains or dyes, such as propidium iodide or4,6-diamidino-2-phenylindole dihydrochloride (DAPI), usually followinghybridization of probes to their target DNAs. Typically, neoplasticcells harbor nuclei that are enlarged, irregular in shape, and/or show amottled staining pattern. Propidium iodide, typically used at aconcentration of about 0.4 μg/ml to about 5 μg/ml, is a red-fluorescingDNA-specific dye that can be observed at an emission peak wavelength of614 nm. DAPI, typically used at a concentration of about 125 ng/ml toabout 1,000 ng/ml, is a blue fluorescing DNA-specific stain that can beobserved at an emission peak wavelength of 452 nm with a DAPI filter atlow magnification. In this case, only those cells pre-selected fordetection are subjected to counting for chromosomal losses and/or gains.Preferably, pre-selected cells on the order of at least 20, and morepreferably at least 30-40, in number are chosen for assessingchromosomal losses and/or gains.

Alternatively, an area evidencing some level of dysplasia or asuspicious lesion can be localized using the DAPI filter at lowmagnification and thoroughly inspected for the presence of nucleiharboring abnormal copy numbers of any probe. In a normal cell, twocopies of a given probe will be detected. In an abnormal cell, more orless copies of a given probe will be detected. Areas with the mostsignificant copy number changes are preferably selected for enumeration.Wherever possible, three abnormal areas are selected and, within eachabnormal area, 10 random nuclei are analyzed under high power (64× or100× objective). Preferably, nuclei are non-overlapping and harborsufficiently bright signals.

Alternatively, cells for detection may be chosen independent ofcytologic or histologic features. For example, all non-overlapping cellsin a given area or areas on a microscope slide may be assessed forchromosomal losses and/or gains. As a further example, cells on theslide, e.g., cells that show altered morphology, on the order of atleast about 50, and more preferably at least about 100, in number thatappear in consecutive order on a microscope slide may be chosen forassessing chromosomal losses and/or gains.

The copies of MYC (8p24), LPL (8p22), PTEN (10q23), and chromosome 8,alone or in further combination with copies of one or more of p16(9p21), chromosome 3, chromosome 7, chromosome 10, and chromosome 17 arecounted, as well as TMPRSS2-ERG or ETV1 Fusions (21q22; 7p21) anddeletions and/or translocations thereof. Additionally, the copies of oneor more of p27Kip1 (4q43), CDK2 (12q13), cyclin E (CCNE1; 19q12 andCCNE2; 8q22), a locus-specific probe for retinoblastoma 1 (Rb1; 13q14),a locus-specific probe for NK3 homeobox 1 (NKX3.1; 8p21.2), alocus-specific probe for epidermal growth factor receptor (EGFR; 7p11),a locus-specific probe for phosphoinositide-3-kinase (PI3K; 3q26), alocus-specific probe for AKT1 kinase (Akt1; 14q32), a locus-specificprobe for FKHR (FOXO1; 13q14.11), a locus-specific probe for p53 bindingprotein homolog (MDM2; 12q14.3-12q15), a locus-specific probe for p53(17p13.1), a locus-specific probe for v-Ki-ras2 Kirsten rat sarcomaviral oncogene homol (KRAS; 12p12.1), a locus-specific probe for v-rafmurine sarcoma viral oncogene homolog B1 (BRAF; 7q34), a locus-specificprobe for cyclin D1 (CCND1; 11q13), a locus-specific probe for B-cellCLL/lymphoma 2 (BCL2; 18q21.3/18q21.33), and a locus-specific probe forandrogen receptor (AR; Xq12) are counted.

Thus, such methods comprise contacting a sample of prostate cellsobtained from a patient, e.g., a nucleic acid sample, with a set ofdetectably labeled probes comprising a locus-specific probe for MYC(8p24), a locus-specific probe for LPL (8p22), a locus-specific probefor PTEN (10q23), and a centromeric probe for chromosome 8, alone or infurther combination with one or more of a locus-specific probe for p16(9p21), TMPRSS2-ERG or ETV1 Fusions (21q22; 7p21), a centromeric probefor chromosome 3, a centromeric probe for chromosome 7, a centromericprobe for chromosome 10, and a centromeric probe for chromosome 17,wherein the set of detectably labeled probes can comprise one or more ofa locus-specific probe for p27Kip1 (4q43), CDK2 (12q13), cyclin E(CCNE1; 19q12 and CCNE2; 8q22), a locus-specific probe forretinoblastoma 1 (Rb1; 13q14), a locus-specific probe for NK3 homeobox 1(NKX3.1; 8p21.2), a locus-specific probe for epidermal growth factorreceptor (EGFR; 7p11), a locus-specific probe forphosphoinositide-3-kinase (PI3K; 3q26), a locus-specific probe for AKT1kinase (Akt1; 14q32), a locus-specific probe for FKHR (FOXO1; 13q14.11),a locus-specific probe for p53 binding protein homolog (MDM2;12q14.3-12q15), a locus-specific probe for p53 (17p13.1), alocus-specific probe for v-Ki-ras2 Kirsten rat sarcoma viral oncogenehomol (KRAS; 12p12.1), a locus-specific probe for v-raf murine sarcomaviral oncogene homolog B1 (BRAF; 7q34), a locus-specific probe forcyclin D1 (CCND1; 11q13), a locus-specific probe for B-cell CLL/lymphoma2 (BCL2; 18q21.3/18q21.33), and a locus-specific probe for androgenreceptor (AR; Xq12)), under conditions that allow (or promote) the probeto bind selectively with its target nucleic acid sequence and form astable hybridization complex. Such methods further comprise detectingthe formation of the hybridization complex and counting the number ofhybridization complexes. In view of the number of hybridizationcomplexes comprising MYC (8p24), LPL (8p22), PTEN (10q23), andchromosome 8, alone or in further combination with the number ofhybridization complexes of one or more of p16 (9p21), TMPRSS2-ERG orETV1 Fusions (21q22; 7p21), chromosome 3, chromosome 7, chromosome 8,chromosome 10, and chromosome 17, alone or in further view of the numberof hybridization complexes comprising one or more of p27Kip1 (4q43),CDK2 (12q13), cyclin E (CCNE1; 19q12 and CCNE2; 8q22), a locus-specificprobe for retinoblastoma 1 (Rb1; 13q14), a locus-specific probe for NK3homeobox 1 (NKX3.1; 8p21.2), a locus-specific probe for epidermal growthfactor receptor (EGFR; 7p11), a locus-specific probe forphosphoinositide-3-kinase (PI3K; 3q26), a locus-specific probe for AKT1kinase (Akt1; 14q32), a locus-specific probe for FKHR (FOXO1; 13q14.11),a locus-specific probe for p53 binding protein homolog (MDM2;12q14.3-12q15), a locus-specific probe for p53 (17p13.1), alocus-specific probe for v-Ki-ras2 Kirsten rat sarcoma viral oncogenehomol (KRAS; 12p12.1), a locus-specific probe for v-raf murine sarcomaviral oncogene homolog B1 (BRAF; 7q34), a locus-specific probe forcyclin D1 (CCND1; 11q13), a locus-specific probe for B-cell CLL/lymphoma2 (BCL2; 18q21.3/18q21.33), and a locus-specific probe for androgenreceptor (AR; Xq12), the method further comprises determining the copynumber of MYC (8p24), LPL (8p22), PTEN (10q23; see, e.g., U.S. Pat. Nos.6,262,242; 6,482,795; and 7,217,795), and chromosome 8, alone or infurther combination with the copy number of one or more of p16 (9p21),chromosome 3, chromosome 7, chromosome 10, and chromosome 17, as well asTMPRSS2-ERG or ETV1 Fusions (21q22; 7p21) and deletions and/ortranslocations thereof, alone or in further combination with the copynumber of one or more of p27Kip1 (4q43), CDK2 (12q13), cyclin E (CCNE1;19q12 and CCNE2; 8q22), a locus-specific probe for retinoblastoma 1(Rb1; 13q14), a locus-specific probe for NK3 homeobox 1 (NKX3.1;8p21.2), a locus-specific probe for epidermal growth factor receptor(EGFR; 7p11), a locus-specific probe for phosphoinositide-3-kinase(PI3K; 3q26), a locus-specific probe for AKT1 kinase (Akt1; 14q32), alocus-specific probe for FKHR (FOXO1; 13q14.11), a locus-specific probefor p53 binding protein homolog (MDM2; 12q14.3-12q15), a locus-specificprobe for p53 (17p13.1), a locus-specific probe for v-Ki-ras2 Kirstenrat sarcoma viral oncogene homol (KRAS; 12p12.1), a locus-specific probefor v-raf murine sarcoma viral oncogene homolog B1 (BRAF; 7q34), alocus-specific probe for cyclin D1 (CCND1; 11q13), a locus-specificprobe for B-cell CLL/lymphoma 2 (BCL2; 18q21.3/18q21.33), and alocus-specific probe for androgen receptor (AR; Xq12). If desired, thecopy number can be compared to a pre-determined cut-off, wherein a copynumber greater than the pre-determined cut-off (i.e., for a gain) and acopy number less than the pre-determined cut-off (i.e., for a loss), asappropriate, indicates that the patient has prostate cancer. When about20% or more of the examined prostate cells from a patient havetranslocations and/or deletions involving TMPRSS2-ERG or ETV1 Fusions(21q22; 7p21), the patient is considered to have prostate cancer.

While deparaffinization, pretreatment, staining, and routine slidewashing also can be conducted in accordance with methods known in theart, use of an automated system, however, such as the VP 2000 Process(Abbott Molecular, Inc., Des Plaines, Ill.), decreases the amount oftime needed to prepare slides for evaluation. Slides can be prepared inlarge batches (e.g., 50 slides), as opposed to small batches (e.g., 4slides) when standard Coplin jars are used for post-hybridizationwashing. In addition, the scoring of slides can be fully automated usingautomated imaging, thereby reducing the amount of hands-on time requiredfor specimen analysis. Full automation also enables the use of animaging algorithm that captures more abnormal cells more frequently andconsistently. Also, while any suitable method of slide preparation knownin the art can be used, slides are preferably prepared using ThinPrep2000 (Hologic, Inc., Bedford, Mass.), which generates more uniform andconsistent monolayers of cells.

Other methods already known in the art or currently under developmentmay require or prefer the use of a sample of prostate cells that isother than cells fixed in formalin and embedded in paraffin, e.g., freshor frozen cells, homogenized cells, lysed cells, or isolated or purifiednucleic acids (e.g., a “nucleic acid sample” such as DNA) from prostatecells (“sample of prostate cells” as used herein is intended toencompass all forms of a sample of prostate cells that enable thedetermination of copy number and gain/loss). Nuclei also can beextracted from thick sections of paraffin-embedded specimens to reducetruncation artifacts and eliminate extraneous embedded material.Typically, biological samples, once obtained, are harvested andprocessed prior to hybridization using standard methods known in theart. Such processing typically includes protease treatment andadditional fixation in an aldehyde solution, such as formaldehyde.

Examples of methods that can be used herein include, but are not limitedto, quantitative polymerase chain reaction (Q-PCR), real-time Q-PCR(Applied Biosystems, Foster City, Calif.), densitometric scanning of PCRproducts, digital PCR, optionally with pre-amplification of the gene(s)and/or chromosomal region(s) for which copy number(s) is/are to bedetermined (see, e.g., Vogelstein et al., PNAS USA 96: 9236-9241 (1999);U.S. Pat. App. Pub. No. 2005/0252773; and U.S. Pat. App. Pub. No.2009/0069194), comparative genomic hybridization (CGH; see, e.g.,Kallioniemi et al., Science 258: 818-821 (1992); and Int'l Pat. App.Pub. No. WO 93/18186), microsatellite or Southern allelotype analysis,dot blots, arrays, microarrays (Carter, Nature Genetics Supplement 39:S16-S21 (July 2007)), multiplex amplifiable probe hybridization (MAPH),multiplex ligation-dependent probe amplification (MLPA; see, e.g.,Schouten et al., Nucleic Acids Res. 30: e 57 (2002)), denaturing highperformance liquid chromatography (dHPLC; Kumar et al., J. Biochem.Biophys. Methods 64(3): 226-234 (2005)), dynamic allele-specifichybridization (DASH), measuring fluorescent probe lengths on combedgenomic DNA (Herrick et al., PNAS 97(1): 222-227 (2000)), referencequery pyrosequencing (RQPS; Liu et al., Cold Spring Harb. Protoc. doi:10.1101/pdb.prot5491 (2010)), mapping of fosmid ends onto a referencesequence (capillary-based technology), microelectrophoretic and nanoporesequencing (see, e.g., Service, Science 311: 1544-1546 (2006); andShendure et al., Nat. Rev. Genet. 5: 335-344 (2004)), and the like.

Denaturation of nucleic acid targets for analysis by in situhybridization and similar methods typically is done in such a manner asto preserve cell morphology. For example, chromosomal DNA can bedenatured by high pH, heat (e.g., temperatures from about 70-95° C.),organic solvents (e.g., formamide), and combinations thereof. Probes, onthe other hand, can be denatured by heat in a matter of minutes.

After denaturation, hybridization is carried out. Conditions forspecifically hybridizing the probes to their nucleic acid targetsgenerally include the combinations of conditions that are employable ina given hybridization procedure to produce specific hybrids, theconditions of which may easily be determined by one of ordinary skill inthe art. Such conditions typically involve controlled temperature,liquid phase, and contact between a probe and a target. Hybridizationconditions vary depending upon many factors including probeconcentration, target length, target and probe G-C content, solventcomposition, temperature, and duration of incubation. At least onedenaturation step can precede contact of the probes with the targets.Alternatively, the probe and the target can be subjected to denaturingconditions together while in contact with one another, or withsubsequent contact of the probe with the biological sample.Hybridization can be achieved with subsequent incubation of theprobe/sample in, for example, a liquid phase of about a 50:50 volumeratio mixture of 2-4×SSC and formamide, at a temperature in the range ofabout 25 to about 55° C. for a time that is illustratively in the rangeof about 0.5 to about 96 hours, or more preferably at a temperature ofabout 32 to about 40° C. for a time in the range of about 2 to about 16hours. In order to increase specificity, a blocking agent, such asunlabeled blocking nucleic acid, as described in U.S. Pat. No. 5,756,696(the contents of which are herein incorporated by reference in theirentirety, and specifically for the description of the use of blockingnucleic acid), can be used. Other conditions can be readily employed forspecifically hybridizing the probes to their nucleic acid targetspresent in the sample, as would be readily apparent to one of skill inthe art. Hybridization protocols are described, for example, in Pinketet al., PNAS USA 85: 9138-9142 (1988); In situ Hybridization Protocols,Methods in Molecular Biology, Vol. 33, Choo, ed., Humana Press, Totowa,N.J. (1994); and Kallioniemi et al., PNAS USA 89: 5321-5325 (1992).

Upon completion of a suitable incubation period, non-specific binding ofchromosomal probes to sample DNA can be removed by a series of washes.Temperature and salt concentrations are suitably chosen for a desiredstringency. The level of stringency required depends on the complexityof a specific probe sequence in relation to the genomic sequence, andcan be determined by systematically hybridizing probes to samples ofknown genetic composition. In general, high stringency washes can becarried out at a temperature in the range of about 65 to about 80° C.with about 0.2× to about 2×SSC and about 0.1% to about 1% of a non-ionicdetergent, such as Nonidet P-40 (NP40). If lower stringency washes arerequired, the washes can be carried out at a lower temperature with anincreased concentration of salt.

When fluorophore-labeled probes or probe compositions are used, thedetection method can involve fluorescence microscopy, flow cytometry, orother means for determining probe hybridization. Any suitablemicroscopic imaging method can be used in conjunction with the methodsdescribed herein for observing multiple fluorophores. In the case wherefluorescence microscopy is employed, hybridized samples can be viewedunder light suitable for excitation of each fluorophore and with the useof an appropriate filter or filters. Automated digital imaging systems,such as the MetaSystems, BioView or Applied Imaging systems,alternatively can be used, along with signal enumeration and dataacquisition algorithms.

Depending on the method employed, a digital image analysis system can beused to facilitate the display of results and to improve the sensitivityof detecting small differences in fluorescence intensity. An exemplarysystem is QUIPS (an acronym for quantitative image processing system),which is an automated image analysis system based on a standardfluorescence microscope equipped with an automated stage, focus controland filter wheel (Ludl Electronic Products, Ltd., Hawthorne, N.Y.). Thefilter wheel is mounted in the fluorescence excitation path of themicroscope for selection of the excitation wavelength. Special filters(Chroma Technology, Brattleboro, Vt.) in the dichroic block allowexcitation of the multiple dyes without image registration shift. Themicroscope has two camera ports, one of which has an intensified CCDcamera (Quantex Corp., Sunnyvale, Calif.) for sensitive high-speed videoimage display, which is used for finding interesting areas on a slide aswell as for focusing. The other camera port has a cooled CCD camera(model 200 by Photometrics Ltd., Tucson, Ariz.), which is used for theactual image acquisition at high resolution and sensitivity. The cooledCCD camera is interfaced to a SUN 4/330 workstation (SUN Microsystems,Inc., Mountain View, Calif.) through a VME bus. The entire acquisitionof multicolor images is controlled using an image processing softwarepackage SCIL-Image (Delft Centre for Image Processing, Delft,Netherlands).

In array CGH (aCGH) the probes are immobilized at distinct locations ona substrate and are not labeled (see, e.g., Int'l Pat. App. Pub. No. WO96/17958). Instead, sample nucleic acids, which comprise target nucleicacid(s), are labeled. Either the sample nucleic acids are labeled priorto hybridization or the hybridization complexes are detectably labeled.In dual- or multi-color aCGH the probe array is simultaneously orsequentially hybridized to two or more collections of differentlylabeled target nucleic acids.

Preferably, biomarker expression is assessed by immunofluorescence (IF)to locate areas for analysis by FISH. IF results closely correlate withFISH abnormalities identified using the probes described herein as wellas morphological assessment of a tumor.

The above methods can be used to stratify patients into those who needrepeat biopsy or intensive follow-up and those who do not. The abovemethods also can be used to distinguish prostate cancer from a benigncondition, such as benign prostatic hyperplasia (BPH). Such methods canbe used in conjunction with other methods, such as histological tissueevaluation, prostate-specific antigen (PSA) detection, nomogram (e.g.,Katan nomogram), methylation, and mutation. In this regard, the methodsalso can be used to confirm diagnosis after radical prostatectomy and todistinguish prostate cancer from a pre-cancerous lesion (e.g., atypicalsmall acinar proliferation in the prostate (ASAP), low-grade prostateintra-epithelial neoplasia (PIN), and high-grade PIN) in the prostateand a pre-cancerous lesion in the prostate from a benign condition, suchas BPH. The methods can aid in the diagnosis of adenocarcinoma in aspecimen obtained by biopsy, trans-urethral resection (TURP), orsurgery, e.g., radical prostatectomy. An advantage of the above methods,particularly in the context of detection and diagnosis, is thatchromosomal abnormalities indicative of prostate cancer can be detectedin cells surrounding a tumor (i.e., “field effect” cells). Thus, even ifthe tumor is missed during biopsy, its presence can be detected inaccordance with the above methods, thereby reducing false negativeresults and the need for repeat biopsies. The methods also can be usedin the prognosis of prostate cancer, the monitoring of the efficacy ofthe prophylactic or therapeutic treatment (e.g., hormone or radiationtherapy) of prostate cancer, and the monitoring of the recurrence ofprostate cancer. The methods can be used to confirm results obtainedwith urine- or blood-based detection methods. The risk of cancer inpatients with pre-cancerous lesions can be assessed using such methods,as well as the aggressiveness of the cancer (e.g., more chromosomalabnormalities and/or more widespread chromosomal abnormalities in thefield effect cells). Such methods also can be used to aid in treatmentdecisions, e.g., active surveillance, surgery, or therapy with hormonesor radiation, and adjuvant treatment decisions, such as in the contextof radical prostatectomy.

Thus, the method can further comprise diagnosing, prognosticating, orassessing the efficacy of a therapeutic/prophylactic treatment of apatient from whom the test sample was obtained. If the method furthercomprises assessing the efficacy of a therapeutic/prophylactic treatmentof the patient from whom the test sample was obtained, the methodoptionally further comprises modifying the therapeutic/prophylactictreatment of the patient as needed to improve efficacy. The method canbe adapted for use in an automated system or a semi-automated system.

Generally, a predetermined level can be employed as a benchmark againstwhich to assess results obtained upon assaying a sample of prostatecells for chromosomal abnormalities. Generally, in making such acomparison, the predetermined level is obtained by running a particularassay a sufficient number of times and under appropriate conditions suchthat a linkage or association of a particular chromosomal abnormality(presence or level) with a particular stage or endpoint of a disease,disorder or condition (e.g., preeclampsia or cardiovascular disease) orwith particular indicia can be made. Typically, the predetermined levelis obtained with assays of reference subjects (or populations ofsubjects).

In particular, with respect to a predetermined level as employed formonitoring disease progression and/or treatment, the chromosomalabnormality (presence or level) may be “unchanged,” “favorable” (or“favorably altered”), or “unfavorable” (or “unfavorably altered”).“Elevated” or “increased” refers to a level of chromosomal abnormalityin a sample of prostate cells that is higher than a typical or normallevel or range (e.g., predetermined level), or is higher than anotherreference level or range (e.g., earlier or baseline sample). The term“lowered” or “reduced” refers to a level of chromosomal abnormality in asample of prostate cells that is lower than a typical or normal level orrange (e.g., predetermined level), or is lower than another referencelevel or range (e.g., earlier or baseline sample). The term “altered”refers to a level of chromosomal abnormality in a sample of prostatecells that is altered (increased or decreased) over a typical or normallevel or range (e.g., predetermined level), or over another referencelevel or range (e.g., earlier or baseline sample).

The typical or normal level or range for a given chromosomal abnormalityis defined in accordance with standard practice. Because the levels ofchromosomal abnormalities in some instances will be very low, aso-called altered level or alteration can be considered to have occurredwhen there is any net change as compared to the typical or normal levelor range, or reference level or range, which cannot be explained byexperimental error or sample variation. Thus, the level measured in aparticular sample will be compared with the level or range of levelsdetermined in similar samples from a so-called normal subject. In thiscontext, a “normal subject” is an individual with no detectable disease,and a “normal” or “control” patient or population is/are one(s) thatexhibit(s) no detectable disease, respectively, for example.Furthermore, given that chromosomal abnormalities are not routinelyfound at high levels in the majority of the human population, a “normalsubject” can be considered an individual with no substantial detectableincreased level of a given chromosomal abnormality, and a “normal”(sometimes termed “control”) patient or population is/are one(s) thatexhibit(s) no substantial detectable increased level of a givenchromosomal abnormality. An “apparently normal subject” is one in whichchromosomal abnormalities have not been or are being assessed. The levelof a given chromosomal abnormality is said to be “elevated” when thechromosomal abnormality is normally undetectable, but is detected in atest sample, as well as when the analyte is present in the test sampleat a higher than normal level. Thus, inter alia, the disclosure providesa method of screening for a subject having, or at risk of having,prostate cancer.

The method can also involve the detection of other markers and the like.For example, the method can also involve the detection ofprostate-specific antigen (PSA), for example.

The methods described herein also can be used to determine whether ornot a subject has or is at risk of developing prostate cancer.Specifically, such a method can comprise the steps of:

(a) determining chromosomal abnormalities in a sample of prostate cellsfrom a subject (e.g., using the methods described herein, or methodsknown in the art); and

(b) comparing the levels of chromosomal abnormalities determined in step(a) with predetermined levels, wherein, if the levels of chromosomalabnormalities determined in step (a) are favorable with respect topredetermined levels, then the subject is determined not to have or beat risk for prostate cancer. However, if the levels of chromosomalabnormalities determined in step (a) are unfavorable with respect topredetermined levels, then the subject is determined to have or be atrisk for prostate cancer.

Additionally, provided herein is method of monitoring the progression ofprostate cancer in a subject. Optimally, the method comprises the stepsof:

(a) determining chromosomal abnormalities in a sample of prostate cellsfrom a subject;

(b) determining the levels of chromosomal abnormalities in a latersample of prostate cells from the subject; and

(c) comparing the levels of chromosomal abnormalities as determined instep (b) with the levels of chromosomal abnormalities as determined instep (a), wherein if the levels in step (b) are unchanged or unfavorablewhen compared to the levels determined in step (a), then prostate canceris determined to have continued, progressed or worsened in the subject.By comparison, if the levels as determined in step (b) are favorablewhen compared to the levels as determined in step (a), then prostatecancer is determined to have discontinued, regressed or improved in thesubject.

Optionally, the method further comprises comparing the levels ofchromosomal abnormalities as determined in step (b), for example, withpredetermined levels. Further, optionally the method comprises treatingthe subject, e.g., with one or more pharmaceutical compositions,radiation, and/or hormone therapy, for a period of time if thecomparison shows that the levels as determined in step (b), for example,are unfavorably altered with respect to the predetermined levels.

Still further, the methods can be used to monitor treatment in a subjectreceiving treatment, e.g., with one or more pharmaceutical compositions,radiation, and/or hormone therapy. Specifically, such methods involveproviding a first sample of prostate cells from a subject before thesubject has been treated. Next, the levels of chromosomal abnormalitiesin the first sample of prostate cells are determined (e.g., using themethods described herein or as known in the art). After the levels ofchromosomal abnormalities are determined, optionally the levels are thencompared with predetermined levels. If the levels as determined in thefirst sample of prostate cells are lower than the predetermined levels,then the subject is not treated. However, if the levels as determined inthe first sample of prostate cells are higher than the predeterminedlevels, then the subject is treated for a period of time. The period oftime that the subject is treated can be determined by one skilled in theart (for example, the period of time can be from about seven (7) days toabout two years, preferably from about fourteen (14) days to about one(1) year).

During the course of treatment, second and subsequent samples ofprostate cells are then obtained from the subject. The number of samplesand the time in which said samples are obtained from the subject are notcritical. For example, a second sample could be obtained seven (7) daysafter the subject is first treated, a third sample could be obtained two(2) weeks after the subject is first treated, a fourth sample could beobtained three (3) weeks after the subject is first treated, a fifthsample could be obtained four (4) weeks after the subject is firsttreated, etc.

After each second or subsequent sample is obtained from the subject, thelevels of chromosomal abnormalities in the second or subsequent sampleare determined (e.g., using the methods described herein or as known inthe art). The levels as determined in each of the second and subsequentsamples are then compared with the levels as determined in the firstsample (e.g., the sample that was originally optionally compared to thepredetermined level). If the levels as determined in step (c) arefavorable when compared to the levels as determined in step (a), thenprostate cancer is determined to have discontinued, regressed orimproved, and the subject should continue to be treated. However, if thelevels determined in step (c) are unchanged or unfavorable when comparedto the levels as determined in step (a), then prostate cancer isdetermined to have continued, progressed or worsened, and the subjectshould be treated with a higher dosage of pharmaceutical composition,radiation, or hormone, for example, or the subject should be treateddifferently.

Generally, for assays in which repeat testing may be done (e.g.,monitoring disease progression and/or response to treatment), a secondor subsequent test sample is obtained at a period in time after thefirst test sample has been obtained from the subject. Specifically, asecond test sample from the subject can be obtained minutes, hours,days, weeks or years after the first test sample has been obtained fromthe subject. For example, the second test sample can be obtained fromthe subject at a time period of about 1 minute, about 5 minutes, about10 minutes, about 15 minutes, about 30 minutes, about 45 minutes, about60 minutes, about 2 hours, about 3 hours, about 4 hours, about 5 hours,about 6 hours, about 7 hours, about 8 hours, about 9 hours, about 10hours, about 11 hours, about 12 hours, about 13 hours, about 14 hours,about 15 hours, about 16 hours, about 17 hours, about 18 hours, about 19hours, about 20 hours, about 21 hours, about 22 hours, about 23 hours,about 24 hours, about 2 days, about 3 days, about 4 days, about 5 days,about 6 days, about 7 days, about 2 weeks, about 3 weeks, about 4 weeks,about 5 weeks, about 6 weeks, about 7 weeks, about 8 weeks, about 9weeks, about 10 weeks, about 11 weeks, about 12 weeks, about 13 weeks,about 14 weeks, about 15 weeks, about 16 weeks, about 17 weeks, about 18weeks, about 19 weeks, about 20 weeks, about 21 weeks, about 22 weeks,about 23 weeks, about 24 weeks, about 25 weeks, about 26 weeks, about 27weeks, about 28 weeks, about 29 weeks, about 30 weeks, about 31 weeks,about 32 weeks, about 33 weeks, about 34 weeks, about 35 weeks, about 36weeks, about 37 weeks, about 38 weeks, about 39 weeks, about 40 weeks,about 41 weeks, about 42 weeks, about 43 weeks, about 44 weeks, about 45weeks, about 46 weeks, about 47 weeks, about 48 weeks, about 49 weeks,about 50 weeks, about 51 weeks, about 52 weeks, about 1.5 years, about 2years, about 2.5 years, about 3.0 years, about 3.5 years, about 4.0years, about 4.5 years, about 5.0 years, about 5.5. years, about 6.0years, about 6.5 years, about 7.0 years, about 7.5 years, about 8.0years, about 8.5 years, about 9.0 years, about 9.5 years or about 10.0years after the first test sample from the subject is obtained.

Moreover, the present disclosure also relates to methods of determiningwhether a subject predisposed to or suffering from prostate cancer willbenefit from treatment. In particular, the disclosure relates tocompanion diagnostic methods and products. Thus, the method of“monitoring the treatment of disease in a subject” as described hereinfurther optimally also can encompass selecting or identifying candidatesfor therapy.

Thus, in particular embodiments, the disclosure also provides a methodof determining whether a subject having, or at risk for, prostate canceris a candidate for therapy. Generally, the subject is one who hasexperienced some symptom of the disease or who has actually beendiagnosed as having, or being at risk for, such a disease, and/or whodemonstrates unfavorable levels of chromosomal abnormalities, asdescribed herein.

The method optionally comprises an assay as described herein, wherelevels of chromosomal abnormalities are assessed before and followingtreatment of a subject. The observation of unfavorable levels ofchromosomal abnormalities following treatment confirms that the subjectwill not benefit from receiving further or continued treatment, whereasthe observation of favorable levels of chromosomal abnormalitiesfollowing treatment confirms that the subject will benefit fromreceiving further or continued treatment. This confirmation assists withmanagement of clinical studies, and provision of improved patient care.

Probes

A set of probes is also provided. In one embodiment, the set of probescomprises a locus-specific probe for MYC (8q24), a locus-specific probefor phosphatase and tensin homolog (PTEN; 10q23), a centromeric probefor chromosome 8, and a centromeric probe for chromosome 7, wherein theset of probes optionally further comprises an anti-α-methylacyl-CoAracemase (AMACR) antibody, which can be detectably labeled. In anotherembodiment, the set of probes comprising a locus-specific probe for MYC(8q24), a locus-specific probe for lipoprotein lipase (LPL; 8p22), alocus-specific probe for PTEN, and a centromeric probe for chromosome 8.The set of probes optionally further comprises an anti-AMACR antibody,which can be detectably labeled. The locus-specific probe for MYC (8q24)preferably covers approximately 820 kb, such as 821 kb, centered on theMYC gene and includes the whole MYC gene as well as adjacent regions(see discussion of “MYC” in method section above). The locus-specificprobe for LPL (8p22) preferably covers approximately 170 kb centered onthe LPL gene and includes the whole LPL gene as well as adjacent regions(see discussion of “LPL” in method section above). The locus-specificprobe for PTEN (10q23) preferably covers approximately 365 to 370 kb,such as 368 kb, centered on the PTEN gene and includes the whole PTENgene as well as adjacent regions, such as STS markers D10S215 on thecentromeric side and RH93626 on the telomeric side (see discussion of“PTEN” in method section above). The set of probes can optionallyfurther comprise one or more of a locus-specific probe for p16 (9p21),TMPRSS2-ERG or ETV1 fusions (21q22; 7p21 locus), a centromeric probe forchromosome 3, a centromeric probe for chromosome 7, a centromeric probefor chromosome 10, and a centromeric probe for chromosome 17. The set ofprobes can further comprise one or more of a locus-specific probe forcyclin-dependent kinase inhibitor p27Kip1 (4q43), a locus-specific probefor CDK2; 12q13), a locus-specific probe for cyclin E (CCNE1; 19q12 andCCNE2; 8q22), a locus-specific probe for retinoblastoma 1 (Rb1; 13q14),a locus-specific probe for NK3 homeobox 1 (NKX3.1; 8p21.2), alocus-specific probe for epidermal growth factor receptor (EGFR; 7p11),a locus-specific probe for phosphoinositide-3-kinase (PI3K; 3q26), alocus-specific probe for AKT1 kinase (Akt1; 14q32), a locus-specificprobe for FKHR (FOXO1; 13q14.11), a locus-specific probe for p53 bindingprotein homolog (MDM2; 12q14.3-12q15), a locus-specific probe for p53(17p13.1), a locus-specific probe for v-Ki-ras2 Kirsten rat sarcomaviral oncogene homolog (KRAS; 12p12.1), a locus-specific probe for v-rafmurine sarcoma viral oncogene homolog B1 (BRAF; 7q34), a locus-specificprobe for cyclin D1 (CCND1; 11q13), a locus-specific probe for B-cellCLL/lymphoma 2 (BCL2; 18q21.3/18q21.33), and a locus-specific probe forandrogen receptor (AR; Xq12).

Suitable probes for use as locus-specific probes hybridize to a specificregion on a chromosome containing a gene. The locus-specific probe forthe gene MYC (8p24) can hybridize to all or a portion of the MYC gene atp24 on chromosome 8 (i.e., 8p24). The locus-specific probe for the geneLPL (8p22) can hybridize to all or a portion of the LPL gene at p22 onchromosome 8 (i.e., 8p22). The locus-specific probe for the gene PTEN(10q23) can hybridize to all or a portion of the PTEN gene at q23 onchromosome 10 (i.e., 10q23). Similarly, the locus-specific probe forp27Kip1 (4q43) can hybridize to all or a portion of the p27Kip1 gene atq43 on chromosome 4 (i.e., 4q43), the locus-specific probe for CDK2(12q13) can hybridize to all or a portion of the CDK2 gene at q13 onchromosome 12 (i.e., 12q13), the locus-specific probe for cyclin E(CCNE1; 19q12 and CCNE2; 8q22) can hybridize to all or a portion of theCCNE1 gene at q12 on chromosome 19 or all or a portion of the CCNE2 geneat q22 on chromosome 8, a locus-specific probe for retinoblastoma 1(Rb1; 13q14) can hybridize to all or a portion of the Rb1 gene at q14 onchromosome 13, a locus-specific probe for NK3 homeobox 1 (NKX3.1;8p21.2) can hybridize to all or a portion of the NKX3.1 gene at p21.2 onchromosome 8, a locus-specific probe for epidermal growth factorreceptor (EGFR; 7p11) can hybridize to all or a portion of the EGFR geneat p11 on chromosome 7, a locus-specific probe forphosphoinositide-3-kinase (PI3K; 3q26) can hybridize to all or a portionof the PI3K gene at q26 on chromosome 3, a locus-specific probe for AKT1kinase (Akt1; 14q32) can hybridize to all or a portion of the Akt1 geneat q32 on chromosome 14, a locus-specific probe for FKHR (FOXO1;13q14.11) can hybridize to all or a portion of the FOXO1 gene at q14.11on chromosome 13, a locus-specific probe for p53 binding protein homolog(MDM2; 12q14.3-12q15) can hybridize to all or a portion of the MDM2 geneat q14.3-q15 on chromosome 12, a locus-specific probe for p53 (17p13.1)can hybridize to all or a portion of the p53 gene at p13.1 on chromosome17, a locus-specific probe for v-Ki-ras2 Kirsten rat sarcoma viraloncogene homolog (KRAS; 12p12.1) can hybridize to all or a portion ofthe KRAS gene at p12.1 on chromosome 12, a locus-specific probe forv-raf murine sarcoma viral oncogene homolog B1 (BRAF; 7q34) canhybridize to all or a portion of the BRAF gene at q34 on chromosome 7, alocus-specific probe for cyclin D1 (CCND1; 11q13) can hybridize to allor a portion of the CCND1 gene at q13 on chromosome 11, a locus-specificprobe for B-cell CLL/lymphoma 2 (BCL2; 18q21.3/18q21.33) can hybridizeto all or a portion of the BCL2 gene at q21.3-q21.33 on chromosome 18,and a locus-specific probe for androgen receptor (AR; Xq12) canhybridize to all or a portion of the AR gene at q12 on chromosome X.

A suitable probe for use as a break-away probe hybridizes to TMPRSS2(21q22), thereby enabling the detection of translocations and/ordeletions.

Suitable probes for use as chromosomal probes hybridize with repetitiveDNA associated with the centromere of a chromosome. Centromeres ofprimate chromosomes contain a complex family of long-tandem repeats ofDNA, which are composed of a monomer repeat length of about 171 basepairs (bp), that is referred to as α-satellite DNA. Chromosomal probesare typically about 50-1×10⁵ nucleotides in length. Longer probestypically are fragmented to about 100-600 nucleotides in length. Theprobe for chromosome 3 can hybridize to the alpha satellite DNA locatedat the centromere of chromosome 3, whereas the probe for chromosome 7can hybridize to alpha satellite DNA located at the centromere ofchromosome 7, the probe for chromosome 8 can hybridize to alphasatellite DNA located at the centromere of chromosome 8, the probe forchromosome 10 can hybridize to alpha satellite DNA located at thecentromere of chromosome 10, and the probe for chromosome 17 canhybridize to the alpha satellite DNA located at the centromere ofchromosome 17. Examples of such probes include CEP3, CEP7, CEP8, CEP 10and CEP17.

Chromosome enumerator probes (CEP) and locus-specific probes that targeta chromosome region or subregion can be obtained commercially or readilyprepared by those in the art. Such probes can be commercially obtainedfrom Abbott Molecular, Inc. (Des Plaines, Ill.), Molecular Probes, Inc.(Eugene, Oreg.), or Cytocell (Oxfordshire, UK). Chromosomal probes canbe prepared, for example, from protein nucleic acids (PNA), cloned humanDNA such as plasmids, bacterial artificial chromosomes (BACs), and P1artificial chromosomes (PACs) that contain inserts of human DNAsequences. A region of interest can be obtained via PCR amplification orcloning. In another embodiment, the chromosomal probes can be oligoprobes. Alternatively, chromosomal probes can be prepared syntheticallyin accordance with methods known in the art.

When targeting of a particular gene locus is desired, probes thathybridize along the entire length of the targeted gene can be preferred,although not required. A locus-specific probe can be designed tohybridize to an oncogene or tumor suppressor gene, the geneticaberration of which is correlated with metastasis, e.g., MYC.

The probes can be prepared by any method known in the art. Probes can besynthesized or recombinantly produced. Such probes can range in lengthfrom about 25,000 base pairs to about 800,000 base pairs.

Preferably, probes are detectably labeled, and each probe is distinctlylabeled. Preferably, the probes are detectably labeled withfluorophores, and each probe is distinctly labeled. Examples ofpreferred fluorophores include, but are not limited to,7-amino-4-methylcoumarin-3-acetic acid (AMCA), 5-carboxy-X-rhodamine,6-carboxy-X-rhodamine, lissamine rhodamine B, 5-carboxyfluorescein,6-carboxyfluorescein, fluorescein-5-isothiocyanate (FITC),7-diethylaminocoumarin-3-carboxylic acid,tetramethylrhodamine-5-isothiocyanate,tetramethylrhodamine-6-isothiocyanate, 5-carboxyltetramethylrhodamine,6-carboxytetramethylrhodamine, 7-hydroxycoumarin-3-carboxylic acid,N-4,4-difluoro-5,7-dimethyl-4-bora-3a,4a-diaza-3-indacenepropionic acid,eosin-5-isothiocyanate, erythrosine-5-isothiocyanate, SPECTRUMRED™(Abbott Molecular, Inc.), SPECTRUMGOLD™ (Abbott Molecular, Inc.),SPECTRUMGREEN™ (Abbott Molecular, Inc.), SPECTRUMAQUA™ (AbbottMolecular, Inc.), TEXAS RED® (Molecular Probes, Inc.), Lucifer yellow,and CASCADE blue® acetylazide (Molecular Probes, Inc.). The particularlabel used is not critical; desirably, however, the particular labeldoes not interfere with in situ hybridization of the probe and thedetection of label on any other probe. The label desirably is detectablein as low copy number as possible to maximize the sensitivity of theassay and be detectable above any background signal. Also desirably, thelabel provides a highly localized signal, thereby providing a highdegree of spatial resolution.

Attachment of fluorophores to nucleic acid probes is well-known in theart and can be accomplished by any available means. Fluorophores can becovalently attached to a particular nucleotide, for example, and thelabeled nucleotide incorporated into the probe using standard techniquessuch as nick translation, random priming (Rigby et al., J. Mol. Biol.113: 237 (1997)), PCR labeling, end labeling, direct labeling bychemical modification of particular residues, such as cytosine residues(U.S. Pat. No. 5,491,224), and the like. Alternatively, the fluorophorecan be covalently attached to nucleotides with activated linker arms,which have been incorporated into the probe, for example, via a linkerto the deoxycytidine nucleotides of the probe that have beentransaminated. Methods for labeling probes are described in U.S. Pat.No. 5,491,224, and Morrison et al., Molecular Cytogenetics: Protocolsand Applications, Chapter 2, “Labeling Fluorescence In SituHybridization Probes for Genomic Targets,” pp. 21-40, Fan, Ed., HumanaPress (2002), both of which are herein incorporated by reference fortheir descriptions of labeling probes.

One of skill in the art will recognize that other agents or dyes can beused in lieu of fluorophores as label-containing moieties. Luminescentagents include, for example, radioluminescent, chemiluminescent,bioluminescent, and phosphorescent label-containing moieties. Agentsthat are detectable with visible light include cyanin dyes.Alternatively, detection moieties that are visualized by indirect meanscan be used. For example, probes can be labeled with biotin ordigoxygenin using routine methods known in the art, and then furtherprocessed for detection. Visualization of a biotin-containing probe canbe achieved via subsequent binding of avidin conjugated to a detectablemarker. The detectable marker may be a fluorophore, in which casevisualization and discrimination of probes can be achieved as describedbelow.

Chromosomal probes hybridized to target regions alternatively can bevisualized by enzymatic reactions of label moieties with suitablesubstrates for the production of insoluble color products. Each probecan be discriminated from other probes within the set by choice of adistinct label moiety. A biotin-containing probe within a set can bedetected via subsequent incubation with avidin conjugated to alkalinephosphatase (AP) or horseradish peroxidase (HRP) and a suitablesubstrate. 5-bromo-4-chloro-3-indolylphosphate and nitro bluetetrazolium (NBT) serve as substrates for alkaline phosphatase, whilediaminobenzoate serves as a substrate for HRP.

Kit

Also provided is a kit. In one embodiment, the kit comprises (a) a setof probes that enables diagnosis of prostate cancer in a patient,wherein the set of probes comprises a locus-specific probe for MYC, alocus-specific probe for phosphatase and tensin homolog (PTEN), acentromeric probe for chromosome 8, and a centromeric probe forchromosome 7, and (b) instructions for diagnosing prostate cancer in apatient, wherein the instructions comprise determining in a sample ofprostate cells obtained from the patient the presence of chromosomalabnormalities. A MYC % gain (% gain is % of cells with MYC>2 signals) ofgreater than 35 (with a range of 2 to 50), a PTEN % loss (% loss is % ofcells with <2 signals) of greater than 33 (with a range of 29 to 33), achromosome 8% gain (% gain is % of cells with >2 signals) of greaterthan 34 (with a range of 32 to 34), and a chromosome 7% abnormal (%abnormal is % of cells with >2 or <2 signals) greater than 28 (with arange of 24 to 29) in a sample of prostate cells from a tumor region ofinterest (ROI) or a benign ROI of the prostate of the patient indicatesthat the patient has prostate cancer. In another embodiment, the kitcomprises (a) a set of probes that enables diagnosis of prostate cancerin a patient and (b) instructions for detecting, diagnosing,prognosticating, or assessing the therapeutic/prophylactic treatment ofprostate cancer in a patient. Thus, the kit can comprise (a) a set ofprobes that enables diagnosis of prostate cancer in a patient, whereinthe set of probes comprises a locus-specific probe for MYC, alocus-specific probe for lipoprotein lipase (LPL), a locus-specificprobe for PTEN, and a centromeric probe for chromosome 8 and (b)instructions for diagnosing prostate cancer in a patient, wherein theinstructions comprise determining in a sample of prostate cells obtainedfrom the patient the presence of chromosomal abnormalities. A MYC/LPL %gain (% gain is % of cells with MYC/LPL>1) of greater than 14 (with arange of 12 to 22), a chromosome 8% abnormal (% abnormal is % of cellswith >2 or <2 signals) of greater than 34 (with a range of 26 to 40), aPTEN % loss (% loss is % of cells with <2 signals) of greater than 44(with a range of 22 to 54), or a MYC/chromosome 8% gain (% gain is % ofcells with MYC/chromosome 8>1) greater than 16 (with a range of 10 to18) in a sample of prostate cells from a tumor ROI of the prostate ofthe patient indicates that the patient has prostate cancer. A MYC/LPL %gain of greater than 18 (with a range of 12 to 19), a chromosome 8%abnormal of greater than 32 (with a range of 25 to 34), a PTEN % loss ofgreater than 26 (with a range of 22 to 28), or a MYC/chromosome 8% gaingreater than 16 (with a range of 9 to 18) in a sample of prostate cellsfrom a benign ROI of the prostate of the patient indicates that thepatient has prostate cancer. The set of probes can further comprise oneor more of a locus-specific probe for p16 (9p21), TMPRSS2-ERG or ETV1fusions (21q22; 7p21 locus), a centromeric probe for chromosome 3, acentromeric probe for chromosome 7, a centromeric probe for chromosome10, and a centromeric probe for chromosome 17. The set of probes canfurther comprise one or more of a locus-specific probe forcyclin-dependent kinase inhibitor p27Kip1 (4q43), a locus-specific probefor CDK2; 12q13), a locus-specific probe for cyclin E (CCNE1; 19q12 andCCNE2; 8q22), a locus-specific probe for retinoblastoma 1 (Rb1; 13q14),a locus-specific probe for NK3 homeobox 1 (NKX3.1; 8p21.2), alocus-specific probe for epidermal growth factor receptor (EGFR; 7p11),a locus-specific probe for phosphoinositide-3-kinase (PI3K; 3q26), alocus-specific probe for AKT1 kinase (Akt1; 14q32), a locus-specificprobe for FKHR (FOXO1; 13q14.11), a locus-specific probe for p53 bindingprotein homolog (MDM2; 12q14.3-12q15), a locus-specific probe for p53(17p13.1), a locus-specific probe for v-Ki-ras2 Kirsten rat sarcomaviral oncogene homolog (KRAS; 12p12.1), a locus-specific probe for v-rafmurine sarcoma viral oncogene homolog B1 (BRAF; 7q34), a locus-specificprobe for cyclin D1 (CCND1; 11q13), a locus-specific probe for B-cellCLL/lymphoma 2 (BCL2; 18q21.3/18q21.33), and a locus-specific probe forandrogen receptor (AR; Xq12). The kit can further comprise instructionsfor morphologically assessing a section of a prostate from a patient andidentifying at least one tumor ROI, at least one benign ROI, or at leastone tumor ROI and at least one benign ROI prior to determining thepresence of chromosomal abnormalities.

Alternatively, the kit can further comprise instructions for assessing asection of a prostate from a patient by immunofluorescence andidentifying the presence of a tumor ROI prior to determining thepresence of chromosomal abnormalities, in which case the kit can furthercomprise an anti-α-methylacyl-CoA racemase (AMACR) antibody, which canbe detectably labeled, and the instructions for assessing a section of aprostate from a patient by immunofluorescence can further comprisecontacting the section with detectably labeled anti-AMACR antibody anddetecting over-expression of AMACR, wherein over-expression of AMACR ina region of the section indicates the presence of a tumor ROI. Theinstructions can further comprise treating the section with heat-inducedepitope retrieval prior to assessing the section of a prostate from apatient by immunofluorescence. Such kits may further comprise blockingagents or other probes, various labels or labeling agents to facilitatedetection of the probes, reagents for hybridization (e.g., buffers), ametaphase spread, and the like.

EXAMPLES

The following examples serve to illustrate the present invention. Theexamples are not intended to limit the scope of the claimed invention inany way.

Example 1

This example describes the analysis of prostate specimens using variouscombinations of probes and fluorescent in situ hybridization (FISH).

Radical prostatectomy specimens from 16 patients with adenocarcinoma ofthe prostate were collected at Rush Medical Center, Chicago, Ill. Twosets of formalin-fixed, paraffin-embedded (FFPE) slides were availablefrom nine patients: one set containing the tumor area scribed by apathologist (tumor region of interest (ROI)) and the other setcontaining an area distant from the tumor (distant ROI). Slides from 11patients with benign prostatic hyperplasia (BPH) were collected bytrans-urethral resection of the prostate (TURP) and used as controls.

The slides were pre-treated by incubation in 1×SSC (15 mM citric acidand 0.15 M NaCl) and subsequent pepsin digestion. The slides werehybridized by multi-color FISH with the following probe sets: MYC, LPL,and chromosome enumerator probe (CEP) 8; PTEN, CEP10®, and CEP7®;TMPRSS2-ERG or ETV1 fusions; and CEP3®, CEP7®, CEP17®, and p16. Severalfields were evaluated. Twenty five to 50 cells/specimen were enumeratedfor the number of fluorescent signals for each probe in the set. Allpatterns of re-arrangement and copy number changes were observed andrecorded for the TMPRSS2 break-away probe. Slides from distant ROI werescanned for most abnormal FISH signal patterns, and the fields of viewcontaining these patterns and the adjacent regions were enumerated.

Tumor ROI in specimens from radical prostatectomy bore chromosomalabnormalities, including MYC amplification/gain, LPL loss, PTEN loss,TMPRSS2 rearrangement, and aneusomy. Significant chromosomalabnormalities were also observed in benign slides containing distantROI. Enumeration results were analyzed to determine a cut-off for eachindividual probe or for a derivative classifier, such as a ratio of twoprobes, which would best discriminate patterns of abnormalitiesassociated with cancer from patterns in apparently benign tissue in theBPH specimens. The cut-off was based on percentage of cells containing agenomic abnormality. A fixed cut-off of a signal count less than thebenign mean signal count minus 3 standard deviations was used toestablish a loss, whereas a fixed cut-off of a signal count greater thanthe benign mean signal count plus three standard deviations was used toestablish a gain. The cut-off for TMPRSS2 rearrangement was greater thanabout 20% of the cells within the evaluated region containing therearrangement. Based on the fixed cut-offs, a gain of MYC and aneusomywere found in 15/16 tumor ROI and TMPRSS2 rearrangement was found in11/16 tumor ROI, whereas a gain of MYC and aneusomy were found in 2/9distant ROI and TMPRSS2 rearrangement was found in 5/9 distant ROI. Theresults of the analysis further demonstrated that the detection ofseveral chromosomal abnormalities at the selected cut-offs was highlyspecific to specimens from adenocarcinoma patients.

Example 2

This example describes the analysis of prostate specimens with FISHusing various combinations of probes.

A total of six probes were used for evaluation. These six probesconsisted of three centromeric probes (CEP®) for chromosomes 7, 8, and10, as well as three locus-specific identifier (LSI®) probes (MYC(8q24), LPL (8p21-22), and PTEN (10q23)). Selection of probes was basedon literature review that revealed frequent aberrations in prostatecancer (Bova et al., Cancer Res. 53: 3869-3873 (1993); Kagan et al.,Oncogene 11: 2121-2126 (1995); Emmert-Buck et al., Cancer Res. 55:2959-2962 (1995); Yoshimoto et al. (2007), supra; and Kazunari et al.,J. Nat'l Cancer Inst. 9(18): 1574-1580 (1999)). LSI® and CEP® probeswere obtained from Vysis/Abbott Molecular, Inc. (Des Plaines, Ill.). Theprobes included for subsequent evaluation were combined into two probesets. The first probe set was ProVysion®, which consisted of MYC 8q24(SpectrumGreen™), LPL 8p21-22 (SpectrumOrange™), and CEP8®(SpectrumAqua™). The second probe set (PTEN set) included PTEN(SpectrumOrange™), CEP7® (SpectrumAqua), and CEP10® (SpectrumGreen).

Thirty-three radical prostatectomy (RP) specimens from patients withadenocarcinoma of the prostate were obtained from Rush UniversityMedical Center, Chicago, Ill. For each specimen, a tissue section of 4-6μm was scribed by a pathologist to mark the tumor region(s). For 17 ofthe 33 RP cases, a second section was available with only histologicallybenign tissue. Twenty-six benign prostatic hyperplasia (BPH) specimensserved as controls (Nakayama et al., J. Cell Biochem. 91(3): 540-552(2004)). FISH signals for each of the 6 probes were enumerated in 50-100cells per section.

For each specimen, a tissue section of 5 μm was scribed by a pathologistto mark tumor region(s), if present. FFPE tissue section slides werebaked at 56° C. for 2-24 hours, pretreated three times in Hemo-De(Scientific Safety Solvents) for 5 minutes each at room temperature,rinsed twice in 100% ethanol for one minute each at room temperature,incubated in 45% formic acid/0.3% hydrogen peroxide for 15 minutes atroom temperature, and then rinsed in deionized water for three minutes.Slides were then incubated in pre-treatment solution (1×SSC, pH 6.3) at80° C. for 35 minutes, rinsed for three minutes in deionized water,incubated for 22 minutes in 0.15% pepsin in 0.1N HCl solution at 37° C.,and rinsed again for three minutes in deionized water. Slides weredehydrated for 1 minute each in 70%, 85%, and 100% ethanol and then airdried. Ten microliters of each respective probe hybridization mix (LSI®buffer, blocking DNA, and labeled probes) were added to the specimens,and a coverslip was applied and sealed with rubber cement. Slides werecodenatured for five minutes at 73° C. and hybridized for 16-24 hours at37° C. on a ThermoBrite (Vysis/Abbott Molecular, Inc.). Followinghybridization, coverslips were removed, and slides were washed in2×SSC/0.3% NP-40 at 73° C. for two minutes and subsequently in2×SSC/0.1% NP-40 for one minute at room temperature. Ten microliters ofDAPI I counterstain were placed on the slide, and a coverslip wasapplied.

Following hybridization, FISH signal enumeration was performed. Eachspecimen was analyzed under a fluorescence microscope using singlebandpass filters (Abbott Molecular, Des Plaines, Ill.) specific for DAPI(4,6-diamidino-2-phenylindole), SpectrumOrange™, SpectrumGreen™, andSpectrumAqua™. The number of FISH signals for each probe was recorded ina minimum of 50 consecutive nonoverlapped, intact interphase nuclei(such as nuclei of about 50-100 cells) in areas of interest, which wereidentified by DAPI staining of nuclei with reference to thecorresponding H&E-stained tissue. The abnormality parameters taken intoaccount for each probe were as follows: Gain: [Signal Count]>2, Loss:[Signal Count]<2, and Abnormal: [Signal Count]>2 or <2. Fixed cut-offswere calculated as “mean of % abnormal cell counts in 26 BPH specimens+3S.D.” Specimen abnormality was defined as “% abnormal cells≧cut-off.”

Abnormal FISH signals were observed on the slides for MYC, LPL, CEP8®,PTEN, CEP10® and CEP7®. Chromosomal abnormalities for MYCamplification/gain, LPL and PTEN loss, and aneusomy were not onlyobserved in tumor regions of interest (ROIs) of specimens from radicalprostatectomy, but also some of the benign ROIs. Table 1 shows thesummary of the enumeration data. Twenty-two out of 33 specimens hadabnormalities that were detected with the ProVysion® probe set (66.7%),and 20 out of 33 specimens had abnormalities that were detected with thePTEN probe set (60.6%). The total abnormality detected for tumor ROIwith ProVysion®+PTEN probe set was 23/33, which is 69.7%. Moreimportantly, a significant number of chromosomal abnormalities wasobserved in 8 out of 17 slides (8/17=47.1%; 4/17=23.5% for ProVysion®;6/17=35.3% PTEN probe set) containing ROI distant (“distant ROI”) from atumor (Table 1). Gain and loss of Chromosome 8 were observedsimultaneously in one specimen among most of the prostate cancer casesanalyzed.

TABLE 1 Chromosomal abnormalities from FISH enumeration data SpecimenTumor ROI (33) Distant ROI (17 of 33) Number ProVysion ® PTEN setProVysion ® PTEN set 01 POS POS POS POS 02 NEG NEG NEG NEG 03 POS POS NA04 NEG NEG NA 05 POS POS NEG NEG 06 NEG NEG NA 07 NEG NEG NEG NEG 08 NEGNEG NA 09 POS NEG NA 10 POS POS NA 11 NEG NEG NEG NEG 12 NEG NEG NEG NEG13 POS POS NEG NEG 14 POS NEG NEG NEG 15 NEG NEG NEG NEG 16 NEG NEG NA17 POS POS NA 18 POS POS POS NEG 19 POS POS NA 20 NEG NEG POS NEG 21 NEGPOS NA 22 POS POS NEG NEG 23 POS POS NA 24 POS NEG NA 25 POS POS NEG POS26 POS POS NA 27 POS POS NEG POS 28 POS POS NA 29 POS POS NEG POS 30 POSPOS NA 31 POS POS NA 32 POS POS POS POS 33 POS POS NEG POS POS =positive NEG = negative

Enumeration results were further analyzed by Receiver OperatingCharacteristic (ROC curve) using SAS version 8.2 (SCA #S05020002). Toselect probes and determine an optimal FISH analysis algorithm yieldingthe highest sensitivity and specificity, the following parameters wereconsidered for each probe:

-   -   % Gain, percent cells with >2 signals,    -   % Loss, percent cells with <2 signals,    -   % Abnormal, percent cells with >2 or <2 signals, and    -   For 2 probe ratios (probe A/probe B), % Gain was percent of        cells with A/B ratio>1, % Loss was percent of cells with A/B        ratio<1.

A combination of MYC/LPL % Gain, PTEN % Loss, MYC/CEP8® % Gain and CEP8®% abnormal parameters within the scribed tumor regions identifiedadenocarcinoma in 97.1% (33/34) of RP specimens, with a specificity of96.2% (25/26) relative to BPH (χ2 p<0.001). When detected in regions ofnormal histology, these abnormalities correlated with adenocarcinoma in82.4% (14/17 RP specimens, χ2 p<0.001 relative to BPH). Table 2 is theROC Analysis Summary of AUC (Area Under the Curve), best specificity andsensitivity for each probe and probe combination.

TABLE 2 ROC Analysis Tumor ROI Benign ROI Probes and Abnormalities AUCSpec Sens AUC Spec Sens MYC/LPL % Gain OR CEP8 0.98 96.2 97.1 0.85 82.480.8 % Abnorm OR PTEN % Loss OR MYC/CEP8 % Gain CEP7/CEP10 % Gain 0.6869.2 58.8 0.62 84.6 47.1 MYC/CEP8 % Gain 0.91 88.5 76.5 0.48 61.5 70.6LPL/CEP8 % Loss 0.85 84.6 82.4 0.60 84.6 47.1 PTEN/CEP10 % Loss * +0.881 80.8 82.4 0.788 80.8 64.7 MYC/LPL % Gain 0.90 96.2 79.4 0.69 80.858.8 CEP7 % Abnorm * + 0.896 80.8 88.2 0.845 80.8 76.5 CEP8 % Abnorm +0.966 88.5 94.1 0.752 76.9 64.7 CEP10 % Abnorm + 0.865 80.8 79.4 0.77573.1 76.5 MYC % Gain * + 0.908 76.9 91.2 0.846 76.9 82.4 LPL % Abnorm +0.945 92.3 79.4 0.736 76.9 64.7 PTEN % Loss * + 0.726 80.8 58.8 0.82780.8 70.6 CEP7 % Gain + 0.886 84.6 85.3 0.77 76.9 70.6 CEP8 % Gain * +0.853 76.9 79.4 0.871 76.9 82.4 CEP10 % Gain + 0.93 84.6 94.1 0.786 84.676.5 AUC = area under the curve Spec = specificity Sens = sensitivity

We also used another method to analyze the data set that is first toscreen for potential important FISH probes by comparing differentspecimen groups (tumor ROI vs. BPH, and benign ROI vs. BPH) usingtwo-sample t-test. FISH parameters with significant p-values(p-value<0.05) from t-test were selected for further examination.

Sixteen parameters derived from genomic copy number detected by FISHwere evaluated. These parameters were CEP10% Abnormal, CEP10% Gain,CEP7% Abnormal, CEP7% Gain, CEP8% Abnormal, CEP8% Gain, CEP8% Loss, MYC% Gain, LPL % Abnormal, LPL % Loss, PTEN % Loss, PTEN/CEP10% Loss,CEP7/CEP10% Gain, LPL/CEP8% Loss, MYC/CEP8% Gain and MYC/LPL % Gain.Results from t-test analyses demonstrated that for all of the 16 FISHparameters, their mean values were statistically different between tumorand BPH groups (Table 3).

TABLE 3 t-Test Comparing Tumor an BPH Tumor BPH FISH ParametersMean(Std) Mean(Std) p-value CEP10% Abnorm 40.03(16.9)  22.92(8.14)<.0001 CEP10% Gain 17.21(20.49)  2.31(4.72) 0.0002 CEP7% Abnorm37.83(16.99) 19.46(6.44) <.0001 CEP7% Gain 15.87(22.22)  1.54(3.93)0.0008 CEP8% Abnorm 47.55(16.02)   23(6.02) <.0001 CEP8% Gain19.97(23.73)  1.54(2.42) <.0001 CEP8% Loss 27.58(15.33) 21.46(5.78)0.0383 MYC % Gain 25.61(29.13)  1.85(2.71) <.0001 LPL % Abnorm57.45(22.86) 22.69(8.58) <.0001 LPL % Loss 46.95(25.91) 21.62(8.69)<.0001 PTEN % Loss 35.38(23.37) 20.92(8.6)  0.0018 PTEN/CEP10% Loss25.54(21.41)  7.85(4.86) <.0001 CEP7/CEP10% Gain 19.72(13.49)12.15(5.36) 0.0047 LPL/CEP8% Loss 35.89(28.69)  8.08(4.18) <.0001MYC/CEP8% Gain 26.12(20.53)  7.77(4.25) <.0001 MYC/LPL % Gain37.52(26.36)  8.08(4.75) <.0001

Results from t-test of benign ROI and BPH data show that 10/16parameters as shown in Table 4 are statistically different for fieldeffect. These ten FISH parameters were CEP10% Abnormal, CEP10% Gain,CEP7% Abnormal, CEP7% Gain, CEP8% Abnormal, CEP8% Gain, MYC % Gain, LPL% Abnormal, PTEN % Loss, and PTEN/CEP10% Loss.

TABLE 4 t-Test Comparing Benign and BPH Benign- BPH- p- FISH ParametersMean(Std) Mean(Std) value Flag CEP10% Abnorm 31.41(9.91)  22.92(8.14)0.0038 Significant CEP10% Gain  5.25(4.44)   2.31(4.72) 0.0469Significant CEP7% Abnorm 29.82(8.57)  19.46(6.44) <.0001 SignificantCEP7% Gain  6.39(6.81)   1.54(3.93) 0.0139 Significant CEP8% Abnorm31.37(12.92) 23(6.02) 0.0210 Significant CEP8% Gain  7.93(6.93) 1.54(2.42) 0.0017 Significant CEP8% Loss 23.44(13)   21.46(5.78) 0.5611MYC % Gain  9.38(8.31)  1.85 (2.71) 0.0019 Significant LPL % Abnorm32.15(12.45) 22.69(8.58) 0.0052 Significant LPL % Loss 24.63(11.4) 21.62(8.69) 0.3312 PTEN % Loss 34.29(16.86) 20.92(8.6) 0.0064Significant PTEN/CEP10% Loss 17.71(16.47)  7.85(4.86) 0.0275 SignificantCEP7/CEP10% Gain 16.65(10.26) 12.15(5.36) 0.1105 LPL/CEP8% Loss11.73(9.45)   8.08(4.18) 0.1487 MYC/CEP8% Gain 13.44(12.84)  7.77(4.25)0.0951 MYC/LPL % Gain 13.97(11.64)  8.08(4.75) 0.0618

The ten FISH parameters, which showed significant difference between BPHand tumor or benign ROI groups based on two-sample t-test, were selectedfor further evaluation. The ROC method was applied to identify theoptimal cut-off value for these FISH parameters. Table 5 summarizes thesensitivity, specificity, and AUC for each of these ten FISH parametersin distinguishing tumor ROI with BPH, as well as distinguishing benignROI with BPH. The top five FISH single parameters were selected based ontheir AUC values in distinguishing benign ROI specimens vs. BPH forfield effect. They were PTEN/CEP10% Loss, PTEN % Loss, CEP7% Abnormal,MYC % Gain and CEP8% Gain, as shown in Table 5.

TABLE 5 Selection of the top five FISH single parameters FISH Para-Tumor - BPH Benign - BPH meters Sensitivity Specificity AUC SensitivitySpecificity AUC CEP8 0.794 0.769 0.853 0.824 0.769 0.871 % Gain MYC0.912 0.769 0.908 0.824 0.769 0.846 % Gain CEP7 0.882 0.808 0.896 0.7650.808 0.845 % Abnorm PTEN 0.588 0.808 0.726 0.706 0.808 0.827 % LossPTEN/ 0.824 0.808 0.881 0.647 0.808 0.788 CEP10 % Loss CEP10 0.941 0.8460.93 0.765 0.846 0.786 % Gain CEP10 0.794 0.808 0.865 0.765 0.731 0.775% Abnorm CEP7 0.853 0.846 0.886 0.706 0.769 0.77 % Gain CEP8 0.941 0.8850.966 0.647 0.769 0.752 % Abnorm LPL 0.794 0.923 0.945 0.647 0.769 0.736% Abnorm

The top five single probe parameters were grouped in all possiblecombinations of four-probe sets, and then analyzed by ReceivingOperating Characteristic (ROC curve) using SAS with cut-offs rangingfrom 5% to 35% by 1% on benign specimens for cut-off values, AUC, aswell as the minimum DFI. For multi-probe combinations, varying cut-offsindependently for each parameter generates a field of points on thegraph, and the points with the highest sensitivity value at eachspecificity value are used to define the ROC curve. While statisticalmethods were used to generate possible combinations and cut-off values,scientific judgment was used to weigh the various trades-offs to resultin the final decision of cut-off values and probe combinations.

The analysis in Table 6 showed that probe set 3 has the largest AUC of0.938, while AUC of probe set 1 is the second largest of 0.917 with theleast DFI, and best sensitivity and specificity. Probe set 3 has onlyone LSI probe, namely PTEN, while probe set 1 has two LSI probes, namelyPTEN and MYC. CEP probes are used to detect aneusomy whereas LSI probesare generally used to detect deletion, duplication, or amplification ofspecific genes. Based on this analysis, probe set 1, including PTEN %loss, CEP7% Abnorm, MYC % gain, and CEP8% Gain, was selected. Thecorresponding sensitivity and specificity of probe set 1 are 0.882 and0.846, respectively.

TABLE 6 ROC analysis of four-probe combinations from the top five singleFISH parameters Probe Cut- Cut- Cut- Cut- Probes Combination Off 1 Off 2Off 3 Off 4 DFI Sens. Spec. AUC Probe PTEN % Loss, 33 28 35 34 0.1940.882 0.846 0.917 Set 1 CEP7 % Abnorm, MYC % Gain, CEP8% Gain ProbePTEN/CEP10 % Loss, 35 25 35 N/A 0.261 0.824 0.808 0.911 Set 2 CEP7 %Abnorm, MYC % Gain Probe PTEN/CEP10 % Loss, 35 25 34 N/A 0.225 0.8820.808 0.938 Set 3 CEP7 % Abnorm, CEP8 % Gain Probe PTEN/CEP10 % Loss, 355 35 N/A 0.371 0.647 0.885 0.834 Set 4 MYC % Gain, CEP8 % Gain

ROC curves plot for the best four-probe combination and the four singleFISH parameters, including PTEN % loss, CEP7% Abnorm, MYC % gain, CEP8%Gain, are shown in FIG. 4. Data were obtained from the FISH evaluationof the 17 benign ROI and 26 BPH specimens. The calculation of thefour-probe combination of the 33 tumor ROI and 26 BPH specimens is alsoshown on the ROC plot. The AUCs of the ROC curves are shown in the tableunder the ROC plot.

Table 7 was the summary of 4-probe combination performance. The cut-offvalues chosen for four individual probe parameters were PTEN % loss>33,CEP7% Abnormal>28, MYC % gain>35, and CEP8% Gain>34. The sensitivity of4-probe combination was 100% and specificity was 84.6% for tumor ROI vs.BPH. While comparing benign ROI with BPH, the probe combination yieldeda sensitivity of 88.2% and a specificity of 84.6%.

TABLE 7 Summary of Four-Probe Combination with Cut-Offs FISH Tumor BPH**Benign BPH** Parameter Sensitivity Specificity AUC SensitivitySpecificity AUC Com- 1.000 0.846 0.960 0.882 0.846 0.917 bination**Combination: PTEN % Loss, CEP7 % Abnorm, MYC % Gain, CEP8 % Gain**Cut-off 1 PTEN % Loss 33; Cut-off 2 CEP7 % Abnorm 28; Cut-off 3 MYC %Gain 35; Cut-off 4 CEP8 % Gain 34

ROC analysis shown in FIG. 5 further defined the cutoff range for eachsingle FISH parameter of the probe set selected.

Comparing to PSA testing, sensitivity for patients with a serum PSAlevel above 4.0 ng/mL is about 20% in contemporary series, and thespecificity of PSA testing is approximately 60% to 70%(Prostate-Specific Antigen Best Practice Statement, 2009 Update,American Urological Association). With FISH test using the 4-probe setselected in this study, 100% sensitivity and 84.6% specificity wereachieved for tumor specimens. Thus, the FISH assay has the potential tooutperform PSA test. With high sensitivity, a negative result can ruleout the possibility of cancer, and further biopsy can be avoided.Moreover, PSA has poorer discriminating ability in men with symptomaticBPH (Meigs et al., J. Gen. Intern. Med. 11: 505 (1996)), while the FISHassay described herein has the potential to detect benign ROIs based onthe field effect with a sensitivity of 88.2% and a specificity of 84.6%.

Another assay used for prostate cancer diagnosis is PCA3 test(Vlaeminck-Guillem et al., Urology 75: 447 (2010)). In four studiesevaluating patients with indeterminate PSA (2.5 to 10.0 ng/mL),sensitivity ranged from 53 to 84 percent and specificity ranged from 71to 80 percent. In three studies with at least 200 patients that provideddata on PCA3 performance following a previous negative biopsy,sensitivity ranged from 47 to 58 percent, and specificity ranged from 71to 72 percent. Although PCA3 has better performance than PSA inindependently predicting a positive biopsy, the performance of thefour-probe FISH assay described herein is better that both PSA and PCA3tests, with 100% sensitivity and 84.6% specificity for tumor specimens,and 88.2% sensitivity and 84.6% specificity for benign ROIs.

In addition to the above, the FISH assay also can be used on cells fromfrozen specimens or cytology specimens. The evaluation includes signaldetection via microscopy or image acquisition, signal enumeration, andsubsequent data analysis algorithms. FISH assay uses stable DNA fordetection of large chromosomal changes (deletion, amplification,aneusomy, and translocation), allows for molecular assessment to becombined with tissue morphology, can detect rare abnormalities inmulti-focal and heterogeneous cancers, can detect the presence of cancerin a biopsy specimen that does not contain actual tumor as accessed byhistological evaluation, can be used as a stand-alone test or as anadjunct to other tests (e.g., histology, PSA, nomogram, methylation, andmutation), and, by combining probes, enables an increase in sensitivityand specificity to be realized as compared to a single analyte assay.

The method may aid histological tissue evaluation to distinguish cancerfrom difficult benign conditions (BPH), to distinguish benign tissuefrom pre-cancerous lesions, and may aid in diagnosis of adenocarcinomain biopsy, trans-urethral resection (TURP), or surgical (radicalprostatectomy) specimens.

In this study with a RP specimen set, chromosomal abnormalities wereobserved within tumor regions as well as within regions of normalhistology extending beyond histologically evident tumor, which confirmedfield canceration effect of prostate cancer. The FISH detection of fieldcanceration may reduce diagnostic biopsy sampling area by discoveringchromosomal abnormalities in field cells apart from an existing cancerthat was missed by the biopsy. Therefore, a molecular test based on FISHto measure MYC, CEP8, PTEN, and CEP7 may allow detection of cancerotherwise missed by histopathological examination and, thus, improve thediagnosis of prostate cancer by reducing sampling error of prostateneedle biopsies.

Example 3

This example describes the analysis of prostate specimens withimmunofluorescence (IF) and FISH using various combinations of probes.

The same FFPE prostate solid tumor tissue slides (Korac et al., J. Clin.Pathol. 58: 1336-1338 (2005)) were analyzed by immunoflourescence andFISH. A specimen pre-treatment/antigen retrieval protocol was developedand optimized for best results on the FFPE tissue.

The first step of this procedure was heat-induced epitope retrieval(HIER). FFPE slides were treated with Hemo-De (Scientific SafetySolvents, Keller, Tex.) for 10 minutes, D-limonene for 10 minutes, twicewith 100% ethanol for two minutes, 85% ethanol for two minutes, 70%ethanol for two minutes, 50% ethanol for two minutes, 30% ethanol fortwo minutes, and water for five minutes. Afterwards, the slides wereheated in sodium citrate buffer, pH 6.0, at 100° C. for 30 minutes,cooled down in sodium citrate buffer, pH 6.0, for 20 minutes, soaked inwater for 5 minutes, and then soaked in phosphate-buffered saline (PBS)for five minutes.

The second step was IF using an anti-α-methylacyl-CoA racemase (AMACR)antibody (Zhong et al., Am. J. Clin. Pathol. 123: 231-236 (2005)) andthe Tyramide Signal Amplification Assay (Sokolova et al., J. Molec.Diag. 9(5): 604-611 (2007)). The Tyramide Solution Assay kit and theAlexa Fluor 488 TSA™ (tyramide signal amplification) kit number 2 withhorseradish peroxidase (HRP) (catalog no. T20912; Invitrogen, Carlsbad,Calif.; Molecular Probes, Eugene, Oreg.) were used in accordance withthe manufacturer's directions. Endogenous peroxidase activity wasblocked by incubation in 3% H₂O₂ for 30 minutes at room temperature.Blocking reagent (100 μL/slide) was added, and slides were incubated ina humidified box for 30 minutes at room temperature. Diluted anti-AMACRantibody (100 μL; rabbit; P504S; clone 13H4; Sigma, St. Louis, Mo.)(diluted in 1% blocking reagent at 1:100) was added, and the slides wereincubated for one hour at room temperature. Slides were washed threetimes for five minutes in PBS/0.1% Tween 20. Stock HRP conjugatesolution was diluted 1:100 in 1% blocking solution. A 100-μL volume ofthis working solution was sufficient to cover a standard 22×22 mmcoverslip. The slides were incubated for 30 minutes at room temperature,washed three times for five minutes in PBS/0.1% Tween 20, and washedonce in PBS. Tyramide solution (100 μL per slide) was added to eachslide, and the slide was incubated for 10 minutes at room temperature inthe dark. Slides were washed for five minutes in PBS and then washed forfive minutes in Milli-Q water.

The third step was FISH. Slides were dehydrated in alcohol (70%, 85% and100%, one minute each) and allowed to air-dry completely. Probe solution(10 μL) was added to each slide, and a coverslip was sealed over theslide with rubber cement. Probe and target DNA were co-denatured at 73°C. for five minutes and hybridized to slides overnight at 37° C.Coverslips were removed by soaking in 2×SSC/0.1% NP-40 at roomtemperature. Slides were washed in 2×SSC/0.3% NP-40 at 73° C. for 2minutes, 2×SSC/0.1% NP-40 at room temperature for one minute, and thenwater, and allowed to air-dry completely in the dark. The slides werecounterstained with DAPI.

Using Tyramide-mediated IF with anti-AMACR antibody in combination withPTEN (SpectrumOrange™) and CEP7® (SpectrumAqua™) FISH probes, sevenspecimens were processed and evaluated. AMACR is a specific marker forcancer cells. It is consistently over-expressed in prostate cancerepithelium. Its expression is also increased in pre-malignant lesions(prostatic intraepithelial neoplasia) (Zhong et al. (2005, supra). AMACRstaining is strongly positive in the tumor ROI, indicating that AMACRprotein is over-expressed. Most cells of this region only have oneallele of PTEN by FISH assay, indicating a PTEN deletion, and twoalleles of CEP 7, indicating that chromosome 7 is intact. The results ofanalysis of the seven specimens are shown in Table 8. The table showsthat 12 out of 14 areas (12/14=85.7%) from seven specimens of the IFstaining (AMACR positive + or negative −) correlated with FISH signalabnormalities of the tested probes, as well as with the morphologicalassessment of tumor by a trained pathologist. In the heterogeneous andmultifocal prostate cancer, AMACR antibody staining identified areas ofinterest for FISH evaluation.

TABLE 8 Immunofluorescence and FISH Analysis. AMACR FISH Specimen SlideType Status (PTEN or CEP7) 23 Tumor (inside scribed) area + Abnormal +Normal − Normal 01 Benign − Normal + Abnormal 15 Tumor − Normal 03Tumor + Abnormal 25 Tumor (inside scribed area) + Abnormal − NormalTumor (outside scribed area) + Abnormal − Normal 10 Tumor (insidescribed area) + Abnormal Tumor (outside scribed area) + Abnormal 18Tumor + Normal

Example 4

This example describes a method of histological sample pretreatment andhybridization for prostate cancer.

FFPE (formalin-fixed paraffin-embedded) histological specimens slides(sections) were baked at 56° C. for 2-24 hours, then were pretreated twoto three times in Hemo-De (Scientific Safety Solvents) or Xyline for 5to 10 minutes each at room temperature followed by two 1-minute rinsesin 100% ethanol at room temperature, incubation in 45% formic acid/0.3%hydrogen peroxide for 15 minutes at room temperature, and a rinse indeionized water for 3-10 minutes. Slides were then incubated inpre-treatment solution (1×SSC, pH 6.3) at 80+/−5° C. for 35-50 minutes,rinsed for 3 minutes in deionized water, incubated 22+/−5 minutes in0.15% pepsin in 0.1N HCl solution at 37° C., and rinsed again for 3minutes in deionized water. Slides were dehydrated for 1 minute each in70%, 85%, and 100% ethanol and then air dried. Ten microliters of eachrespective probe hybridization mix (LSI® buffer, blocking DNA, labeledprobes) were added to the specimens, and a coverslip was applied andsealed with rubber cement. Slides were codenatured for 5 minutes at73+/−2° C. and hybridized for 10-24 hours at 37° C. on a ThermoBrite(Vysis/Abbott Molecular, Inc.). Following hybridization, coverslips wereremoved. The sample was placed in a wash solution consisting of0.3×-2×SSC & 0.3%-0.5% NP-40, and the temperature of the sample wasraised to about 73° C. for about 2-5 minutes. Then the support carryingthe sample was counterstained with a nuclear DNA-binding stain, such as4′,6-diamidino-2-phenylindole (DAPI) either in solution, or upon dryingthe sample in the dark. In the latter case, the sample wascounterstained with about 10 μL DAPI, and a new coverslip was placedover the sample. The sample was then viewed or stored, e.g., at about−20° C.

Example 5

This example describes a method of prostate FFPE slide IF-FISHprocedure.

For the assay of simultaneous FISH and Immunofluorescence (IF) on thesame FFPE prostate solid tumor tissue slides, a specimenpre-treatment/antigen retrieval protocol was developed and optimized forbest results on the FFPE tissue for IF-FISH.

The first step of this procedure is antigen retrieval. Prostate cancerFFPE slides were baked at 56° C. for 2 hours to overnight. Slides werethen de-paraffinized by two immersion in Hemo-De for 10 minutes each.Slides were then incubated in 100% ethanol for 2 minutes twice. Slideswere hydrated by placement in 85%, 70%, 50%, and 30% ethanol for 2minutes each. A final 5-minute immersion in molecular grade Milli-Qwater was carried out. A water bath was pre-heated with a Coplin jarcontaining sodium citrate buffer (10 mM sodium citrate, 0.05% Tween 20,pH 6.0) until the temperature reached 96+/−4° C. Slides were incubatedfor 20-60 minutes. Slides were cooled at room temperature for 20-40minutes on the bench. Slides were washed for five minutes in Milli-Qwater and rinsed once for five minutes in PBS.

The second step is the immunoflorescence (IF) with AMACR antibody andTyramide Signal Amplification Assay. The Tyramide Solution Assay (TSA)kit and the Alexa Fluor 488 TSA (tyramide signal amplification) kitnumber 2 (Invitrogen, Molecular Probes) were used following themanufacturer's directions. Endogenous peroxidase activity was blocked byincubation in 3% H₂O₂ for 30 minutes at room temperature. Blockingreagent (100 μL/slide) was added with incubation in a humidified box for30 minutes at room temperature. Added were 100 uL of diluted AMACRrabbit antibody (diluted in 1% blocking reagent at 1:100) withincubation for 1 hour at room temperature. Slides were washed for fiveminutes three times in PBS/0.1% Tween 20. The stock HRP conjugatesolution was diluted 1:100 in 1% blocking solution. A 100 μL volume ofthis working solution is sufficient to cover a standard 22×22 mmcoverslip. The slides were incubated for 30 minutes at room temperature.Slides were washed for three times for five minutes each in PBS/0.1%Tween 20 and then washed once in PBS. Added were 100 μL of tyramidesolution per slide followed by incubation for 10 minutes at roomtemperature in the dark. Slides were then washed for five minutes in PBSand five minutes in Milli-Q water.

The third step is FISH assay. Slides were dehydrated in alcohol (70%,85% and 100%, one minute each), and allowed to air dry completely. Addedwere 10 μL of probe solution to each slide, and the coverslips weresealed over the slides with rubber cement. Probe and target DNA weredenatured at 73° C. for 5 minutes followed by hybridization overnight at37° C. The sample was placed in the wash solution consisting of0.3×-2×SSC and 0.3%-0.5% NP-40, and the temperature of the sample wasraised to about 73° C. for about 2-5 minutes. Then the support carryingthe sample was counterstained with a nuclear DNA-binding stain, such as4′,6-diamidino-2-phenylindole (DAPI), either in solution or upon dryingthe sample in the dark. In the latter case, the sample wascounterstained with about 10 μL DAPI, and a new coverslip was placedover the sample. The sample was then viewed or stored, e.g., at about−20° C.

All patents, patent application publications, journal articles,textbooks, and other publications mentioned in the specification areindicative of the level of skill of those in the art to which thedisclosure pertains. All such publications are incorporated herein byreference to the same extent as if each individual publication werespecifically and individually indicated to be incorporated by reference.

The invention illustratively described herein may be suitably practicedin the absence of any element(s) or limitation(s), which is/are notspecifically disclosed herein. Thus, for example, each instance hereinof any of the terms “comprising,” “consisting essentially of,” and“consisting of” may be replaced with either of the other two terms.Likewise, the singular forms “a,” “an,” and “the” include pluralreferences unless the context clearly dictates otherwise. Thus, forexample, references to “the method” includes one or more methods and/orsteps of the type, which are described herein and/or which will becomeapparent to those ordinarily skilled in the art upon reading thedisclosure.

The terms and expressions, which have been employed, are used as termsof description and not of limitation. In this regard, where certainterms are defined under “Definitions” and are otherwise defined,described, or discussed elsewhere in the “Detailed Description,” allsuch definitions, descriptions, and discussions are intended to beattributed to such terms. There also is no intention in the use of suchterms and expressions of excluding any equivalents of the features shownand described or portions thereof. Furthermore, while subheadings, e.g.,“Definitions,” are used in the “Detailed Description,” such use issolely for ease of reference and is not intended to limit any disclosuremade in one section to that section only; rather, any disclosure madeunder one subheading is intended to constitute a disclosure under eachand every other subheading.

It is recognized that various modifications are possible within thescope of the claimed invention. Thus, it should be understood that,although the present invention has been specifically disclosed in thecontext of preferred embodiments and optional features, those skilled inthe art may resort to modifications and variations of the conceptsdisclosed herein. Such modifications and variations are considered to bewithin the scope of the invention as claimed herein.

What is claimed is:
 1. A method of detecting prostate cancer in apatient, which method comprises: (a) contacting a sample of prostatecells from the patient with a set of detectably labeled probescomprising a locus-specific probe for MYC, a locus-specific probe forphosphatase and tensin homolog (PTEN), a centromeric probe forchromosome 8, and a centromeric probe for chromosome 7 underhybridization conditions; (b) determining the percentage of cells from atumor region of interest (ROI) or a benign ROI in the sample having copynumber gains in MYC, chromosome 8, and chromosome 7 and copy numberlosses in PTEN and chromosome 7; (c) diagnosing prostate cancer in thepatient by detecting greater than 35% of cells have a MYC signal ofgreater than 2, greater than 33% of cells have a PTEN signal of lessthan 2, greater than 34% of cells have a chromosome 8 signal of greaterthan 2, and greater than 28% of cells have greater than 2 or less than 2chromosome 7 signals in the sample of prostate cells; and (d)administering treatment with, radiation, and/or hormone therapy to thepatient diagnosed as having prostate cancer.
 2. The method of claim 1,wherein the sample of prostate cells is a section of the prostate of thepatient.
 3. The method of claim 2, wherein the section is formalin-fixedand paraffin-embedded and placed on a microscope slide.
 4. The method ofclaim 3, wherein, prior to determining the presence of chromosomal gainsand/or losses, the method further comprises morphologically assessingthe section and identifying at least one tumor ROI, at least one benignROI, or at least one tumor ROI and at least one benign ROI.
 5. Themethod of claim 3, wherein, prior to determining the presence ofchromosomal gains and/or losses, the method further comprises assessingthe section by immunofluorescence and identifying at least one tumorROI.
 6. The method of claim 5, wherein assessing the section byimmunofluorescence comprises contacting the section with a detectablylabeled anti- α- methylacyl-CoA racemase (AMACR) antibody and detectingover-expression of AMACR, wherein over-expression of AMACR in a regionof the section indicates the presence of a tumor ROI.
 7. The method ofclaim 6, wherein, prior to assessing the section by immunofluorescence,the method further comprises treating the section with heat-inducedepitope retrieval.
 8. The method of claim 1, which comprises determiningchromosomal abnormalities in a tumor ROI.
 9. The method of claim 1,which comprises determining chromosomal abnormalities in a benign ROI.